Pages 1–8 1ujm Evolutionary trace report by report maker February 28, 2010

4.3.3 DSSP 8 4.3.4 HSSP 8 4.3.5 LaTex 8 4.3.6 Muscle 8 4.3.7 Pymol 8 4.4 Note about ET Viewer 8 4.5 Citing this work 8 4.6 About report maker 8 4.7 Attachments 8

1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1ujm): Title: Crystal structure of aldehyde reductase 2 from sporobolomy- ces salmonicolor aku4429 Compound: Mol id: 1; molecule: aldehyde reductase ii; chain: a, b; synonym: aldehyde reductase 2, arii; ec: 1.1.1.2; engineered: yes Organism, scientific name: Sporobolomyces Salmonicolor; 1ujm contains a single unique chain 1ujmA (342 residues long) and its homologue 1ujmB.

2 CHAIN 1UJMA CONTENTS 2.1 Q9UUN9 overview 1 Introduction 1 From SwissProt, id Q9UUN9, 96% identical to 1ujmA: Description: Aldehyde reductase II (EC 1.1.1.2) (ARII). 2 Chain 1ujmA 1 Organism, scientific name: Sporobolomyces salmonicolor. 2.1 Q9UUN9 overview 1 Taxonomy: Eukaryota; Fungi; Basidiomycota; Urediniomycetes; 2.2 Multiple sequence alignment for 1ujmA 1 Microbotryomycetidae; Sporidiobolales; Sporidiobolus. 2.3 Residue ranking in 1ujmA 1 Function: Catalyzes the asymmetric reduction of o-substituted ali- 2.4 Top ranking residues in 1ujmA and their position on phatic and aromatic aldehydes and ketones to an S-enantiomer. Redu- the structure 1 ces ethyl 4-chloro-3-oxobutanoate to ethyl (S)-4-chloro-3- hydroxy- 2.4.1 Clustering of residues at 25% coverage. 2 butanoate. 2.4.2 Overlap with known functional surfaces at Catalytic activity: An alcohol + NADP(+) = an aldehyde + NADPH. 25% coverage. 2 Enzyme regulation: Inhibited by quercetin and diphenylhydantoin. Biophysicochemical properties: 3 Notes on using trace results 6 pH dependence: Optimum pH is 5.5; Temperature dependence: 3.1 Coverage 6 Optimum temperature is 40 degrees Celsius; 3.2 Known substitutions 6 Subunit: Monomer. 3.3 Surface 6 Similarity: Belongs to the dihydroflavonol-4-reductase family. 3.4 Number of contacts 7 About: This Swiss-Prot entry is copyright. It is produced through a 3.5 Annotation 7 collaboration between the Swiss Institute of Bioinformatics and the 3.6 Mutation suggestions 7 EMBL outstation - the European Bioinformatics Institute. There are no restrictions on its use as long as its content is in no way modified 4 Appendix 7 and this statement is not removed. 4.1 File formats 7 4.2 Color schemes used 7 2.2 Multiple sequence alignment for 1ujmA 4.3 Credits 7 For the chain 1ujmA, the alignment 1ujmA.msf (attached) with 144 4.3.1 Alistat 7 sequences was used. The alignment was downloaded from the HSSP 4.3.2 CE 8 database, and fragments shorter than 75% of the query as well as

1 Lichtarge lab 2006 2.4 Top ranking residues in 1ujmA and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 3 shows residues in 1ujmA colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment.

Fig. 1. Residues 2-172 in 1ujmA colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.)

Fig. 2. Residues 173-343 in 1ujmA colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.)

duplicate sequences were removed. It can be found in the attachment to this report, under the name of 1ujmA.msf. Its statistics, from the alistat program are the following: Fig. 3. Residues in 1ujmA, colored by their relative importance. Clockwise: front, back, top and bottom views. Format: MSF Number of sequences: 144 Total number of residues: 44966 Smallest: 266 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Largest: 342 top 25% of all residues, this time colored according to clusters they Average length: 312.3 belong to. The clusters in Fig.4 are composed of the residues listed Alignment length: 342 in Table 1. Average identity: 31% Table 1. Most related pair: 99% cluster size member Most unrelated pair: 16% color residues Most distant seq: 32% red 83 15,16,17,18,19,20,21,22,23 24,25,26,27,32,33,36,37,39 Furthermore, <1% of residues show as conserved in this ali- 40,41,42,43,44,45,48,71,72 gnment. 77,78,82,84,88,90,91,92,93 The alignment consists of 26% eukaryotic ( 9% fungi, 16% plan- 94,107,108,111,112,114,115 tae) sequences. (Descriptions of some sequences were not readily 116,118,119,125,126,127,128 available.) The file containing the sequence descriptions can be found 129,131,132,133,150,151,154 in the attachment, under the name 1ujmA.descr. 155,177,179,180,181,184,185 188,189,191,199,201,202,205 206,209,211,212,248,249,250 2.3 Residue ranking in 1ujmA 252,254,256,257,270 The 1ujmA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues Table 1. Clusters of top ranking residues in 1ujmA. in 1ujmA can be found in the file called 1ujmA.ranks sorted in the attachment.

2 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) V(20) L(9)A .(1) M(1)

Table 2. The top 25% of residues in 1ujmA at the interface with sulfate ion.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the num- ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. )

Table 3. res type disruptive mutations 22 G (KR)(E)(FMWH)(Q) 93 S (R)(K)(H)(FW) Fig. 4. Residues in 1ujmA, colored according to the cluster they belong to: 25 A (R)(KYE)(H)(QD) red, followed by blue and yellow are the largest clusters (see Appendix for 23 F (K)(E)(Q)(TD) the coloring scheme). Clockwise: front, back, top and bottom views. The 24 V (R)(K)(Y)(E) corresponding Pymol script is attached. Table 3. List of disruptive mutations for the top 25% of residues in 1ujmA, that are at the interface with sulfate ion. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Sulfate ion binding site. By analogy with 1ujmB – 1ujmSO41009 interface. Table 2 lists the top 25% of residues at the interface with 1ujmSO41009 (sulfate ion). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 22 G G(97) 0.02 9/9 3.26 S(1) .(1) 93 S S(81) 0.07 1/0 4.83 T(9)M G(2) C(2)PN H(2). 25 A G(17) 0.09 1/1 4.86 .(2) A(79)P 23 F F(63) 0.14 23/13 2.59 Y(30) .(1) L(4) 24 V I(65) 0.19 7/5 2.88 Y(1) Fig. 5. Residues in 1ujmA, at the interface with sulfate ion, colored by their continued in next column relative importance. The ligand (sulfate ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1ujmA.)

3 Figure 5 shows residues in 1ujmA colored by their importance, at the Figure 6 shows residues in 1ujmA colored by their importance, at the interface with 1ujmSO41009. interface with 1ujmSO41004. Sulfate ion binding site. Table 4 lists the top 25% of residues Sulfate ion binding site. Table 6 lists the top 25% of residues at the interface with 1ujmSO41004 (sulfate ion). The following table at the interface with 1ujmSO41001 (sulfate ion). The following table (Table 5) suggests possible disruptive replacements for these residues (Table 7) suggests possible disruptive replacements for these residues (see Section 3.6). (see Section 3.6).

Table 4. Table 6. res type subst’s cvg noc/ dist res type subst’s cvg noc/ dist ˚ (%) bb (A) (%) bb (A˚ ) 252 D D(88) 0.08 1/0 4.62 26 S A(11) 0.14 1/1 4.59 N(2). .(2) E(3) S(66) S(3)VHA G(4)T Q(9) Table 4. The top 25% of residues in 1ujmA at the interface with sulfate L(1)V ion.(Field names: res: residue number in the PDB entry; type: amino acid I(2)K type; substs: substitutions seen in the alignment; with the percentage of each 250 A V(75) 0.14 5/4 3.48 type in the bracket; noc/bb: number of contacts with the ligand, with the num- A(6) ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) I(6) D(1). H(2)Y Table 5. T(1) res type disruptive S(2) mutations L(2)CN 252 D (R)(H)(FW)(Y) 27 H H(36) 0.21 28/11 3.02 .(2) W(45)A Table 5. List of disruptive mutations for the top 25% of residues in 1ujmA, that are at the interface with sulfate ion. V(2) L(2) Y(1) T(1) Q(3) R(1) N(1)SC

Table 6. The top 25% of residues in 1ujmA at the interface with sulfate ion.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the num- ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. )

Table 7. res type disruptive mutations 26 S (R)(K)(H)(FW) 250 A (R)(K)(E)(Y) 27 H (E)(D)(Q)(M)

Table 7. List of disruptive mutations for the top 25% of residues in 1ujmA, that are at the interface with sulfate ion.

Fig. 6. Residues in 1ujmA, at the interface with sulfate ion, colored by their relative importance. The ligand (sulfate ion) is colored green. Atoms further Figure 7 shows residues in 1ujmA colored by their importance, at the than 30A˚ away from the geometric center of the ligand, as well as on the line interface with 1ujmSO41001. of sight to the ligand were removed. (See Appendix for the coloring scheme Sulfate ion binding site. Table 8 lists the top 25% of residues for the protein chain 1ujmA.) at the interface with 1ujmSO41002 (sulfate ion). The following table

4 Table 9. res type disruptive mutations 44 R (T)(D)(CG)(Y) 21 N (Y)(H)(FW)(R) 48 K (Y)(FW)(T)(CHG)

Table 9. List of disruptive mutations for the top 25% of residues in 1ujmA, that are at the interface with sulfate ion.

Fig. 7. Residues in 1ujmA, at the interface with sulfate ion, colored by their relative importance. The ligand (sulfate ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1ujmA.)

(Table 9) suggests possible disruptive replacements for these residues (see Section 3.6).

Table 8. res type subst’s cvg noc/ dist Fig. 8. Residues in 1ujmA, at the interface with sulfate ion, colored by their (%) bb (A˚ ) relative importance. The ligand (sulfate ion) is colored green. Atoms further 44 R R(97). 0.01 14/1 3.04 than 30A˚ away from the geometric center of the ligand, as well as on the line I(1) of sight to the ligand were removed. (See Appendix for the coloring scheme 21 N T(20) 0.15 9/0 2.70 for the protein chain 1ujmA.) S(39) N(25) G(11) Figure 8 shows residues in 1ujmA colored by their importance, at the A(2) interface with 1ujmSO41002. .(1) Sulfate ion binding site. Table 10 lists the top 25% of resi- 48 K K(46) 0.20 14/0 3.02 dues at the interface with 1ujmSO41003 (sulfate ion). The following N(13) table (Table 11) suggests possible disruptive replacements for these A(2) residues (see Section 3.6). D(20) Table 10. R(3) res type subst’s cvg noc/ dist S(4) (%) bb (A˚ ) P(2) 212 T P(80) 0.14 6/0 3.75 G(1)IE. A(2) Q(2) L(1) T(4) Table 8. The top 25% of residues in 1ujmA at the interface with sulfate E(3)I ion.(Field names: res: residue number in the PDB entry; type: amino acid R(2)K type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the num- continued in next column ber of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. )

5 Table 10. continued Table 12. res type subst’s cvg noc/ dist res type subst’s cvg noc/ dist (%) bb (A˚ ) (%) bb (A˚ ) G(1) 191 F F(74) 0.08 2/0 4.17 .(1)D W(9) I(4) Table 10. The top 25% of residues in 1ujmA at the interface with sulfate Y(4) ion.(Field names: res: residue number in the PDB entry; type: amino acid .(5) type; substs: substitutions seen in the alignment; with the percentage of each E(1)M type in the bracket; noc/bb: number of contacts with the ligand, with the num- ber of contacts realized through backbone atoms given in the bracket; dist: Table 12. The top 25% of residues in 1ujmA at the interface with 1ujmB. distance of closest apporach to the ligand. ) (Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the number of Table 11. contacts realized through backbone atoms given in the bracket; dist: distance res type disruptive of closest apporach to the ligand. ) mutations 212 T (R)(KH)(FW)(Q)

Table 11. List of disruptive mutations for the top 25% of residues in Table 13. 1ujmA, that are at the interface with sulfate ion. res type disruptive mutations 191 F (K)(E)(T)(Q)

Table 13. List of disruptive mutations for the top 25% of residues in 1ujmA, that are at the interface with 1ujmB.

Fig. 9. Residues in 1ujmA, at the interface with sulfate ion, colored by their relative importance. The ligand (sulfate ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1ujmA.)

Figure 9 shows residues in 1ujmA colored by their importance, at the Fig. 10. Residues in 1ujmA, at the interface with 1ujmB, colored by their interface with 1ujmSO41003. relative importance. 1ujmB is shown in backbone representation (See Appen- Interface with 1ujmB.Table 12 lists the top 25% of residues at dix for the coloring scheme for the protein chain 1ujmA.) the interface with 1ujmB. The following table (Table 13) suggests possible disruptive replacements for these residues (see Section 3.6). Figure 10 shows residues in 1ujmA colored by their importance, at the interface with 1ujmB.

6 3 NOTES ON USING TRACE RESULTS 3.6 Mutation suggestions 3.1 Coverage Mutation suggestions are completely heuristic and based on comple- Trace results are commonly expressed in terms of coverage: the resi- mentarity with the substitutions found in the alignment. Note that due is important if its “coverage” is small - that is if it belongs to they are meant to be disruptive to the interaction of the protein some small top percentage of residues [100% is all of the residues with its ligand. The attempt is made to complement the following in a chain], according to trace. The ET results are presented in the properties: small [AV GSTC], medium [LPNQDEMIK], large form of a table, usually limited to top 25% percent of residues (or [WFYHR], hydrophobic [LPVAMWFI], polar [GTCY ]; posi- to some nearby percentage), sorted by the strength of the presumed tively [KHR], or negatively [DE] charged, aromatic [WFYH], evolutionary pressure. (I.e., the smaller the coverage, the stronger the long aliphatic chain [EKRQM], OH-group possession [SDETY ], pressure on the residue.) Starting from the top of that list, mutating a and NH2 group possession [NQRK]. The suggestions are listed couple of residues should affect the protein somehow, with the exact according to how different they appear to be from the original amino effects to be determined experimentally. acid, and they are grouped in round brackets if they appear equally disruptive. From left to right, each bracketed group of amino acid 3.2 Known substitutions types resembles more strongly the original (i.e. is, presumably, less disruptive) These suggestions are tentative - they might prove disrup- One of the table columns is “substitutions” - other amino acid types tive to the fold rather than to the interaction. Many researcher will seen at the same position in the alignment. These amino acid types choose, however, the straightforward alanine mutations, especially in may be interchangeable at that position in the protein, so if one wants the beginning stages of their investigation. to affect the protein by a point mutation, they should be avoided. For example if the substitutions are “RVK” and the original protein has 4 APPENDIX an R at that position, it is advisable to try anything, but RVK. Conver- sely, when looking for substitutions which will not affect the protein, 4.1 File formats one may try replacing, R with K, or (perhaps more surprisingly), with Files with extension “ranks sorted” are the actual trace results. The V. The percentage of times the substitution appears in the alignment fields in the table in this file: is given in the immediately following bracket. No percentage is given in the cases when it is smaller than 1%. This is meant to be a rough • alignment# number of the position in the alignment guide - due to rounding errors these percentages often do not add up • residue# residue number in the PDB file to 100%. • type amino acid type • 3.3 Surface rank rank of the position according to older version of ET • variability To detect candidates for novel functional interfaces, first we look for has two subfields: residues that are solvent accessible (according to DSSP program) by 1. number of different amino acids appearing in in this column 2 at least 10A˚ , which is roughly the area needed for one water mole- of the alignment cule to come in the contact with the residue. Furthermore, we require 2. their type that these residues form a “cluster” of residues which have neighbor • rho ET score - the smaller this value, the lesser variability of within 5A˚ from any of their heavy atoms. this position across the branches of the tree (and, presumably, Note, however, that, if our picture of protein evolution is correct, the greater the importance for the protein) the neighboring residues which are not surface accessible might be • cvg coverage - percentage of the residues on the structure which equally important in maintaining the interaction specificity - they have this rho or smaller should not be automatically dropped from consideration when choo- • sing the set for mutagenesis. (Especially if they form a cluster with gaps percentage of gaps in this column the surface residues.) 4.2 Color schemes used 3.4 Number of contacts The following color scheme is used in figures with residues colored by cluster size: black is a single-residue cluster; clusters composed of Another column worth noting is denoted “noc/bb”; it tells the num- more than one residue colored according to this hierarchy (ordered ber of contacts heavy atoms of the residue in question make across by descending size): red, blue, yellow, green, purple, azure, tur- the interface, as well as how many of them are realized through the quoise, brown, coral, magenta, LightSalmon, SkyBlue, violet, gold, backbone atoms (if all or most contacts are through the backbone, bisque, LightSlateBlue, orchid, RosyBrown, MediumAquamarine, mutation presumably won’t have strong impact). Two heavy atoms DarkOliveGreen, CornflowerBlue, grey55, burlywood, LimeGreen, A˚ are considered to be “in contact” if their centers are closer than 5 . tan, DarkOrange, DeepPink, maroon, BlanchedAlmond. The colors used to distinguish the residues by the estimated 3.5 Annotation evolutionary pressure they experience can be seen in Fig. 11. If the residue annotation is available (either from the pdb file or from other sources), another column, with the header “annotation” 4.3 Credits appears. Annotations carried over from PDB are the following: site 4.3.1 Alistat alistat reads a multiple sequence alignment from the (indicating existence of related site record in PDB ), S-S (disulfide file and shows a number of simple statistics about it. These stati- bond forming residue), hb (hydrogen bond forming residue, jb (james stics include the format, the number of sequences, the total number bond forming residue), and sb (for salt bridge forming residue). of residues, the average and range of the sequence lengths, and the

7 ”MUSCLE: multiple sequence alignment with high accuracy and high throughput.” Nucleic Acids Research 32(5), 1792-97. http://www.drive5.com/muscle/

COVERAGE 4.3.7 Pymol The figures in this report were produced using Pymol. The scripts can be found in the attachment. Pymol V is an open-source application copyrighted by DeLano Scien- 100% 50% 30% 5% tific LLC (2005). For more information about Pymol see http://pymol.sourceforge.net/. (Note for Windows users: the attached package needs to be unzipped for Pymol to read the scripts and launch the viewer.) 4.4 Note about ET Viewer V Dan Morgan from the Lichtarge lab has developed a visualization RELATIVE IMPORTANCE tool specifically for viewing trace results. If you are interested, please visit:

Fig. 11. Coloring scheme used to color residues by their relative importance. http://mammoth.bcm.tmc.edu/traceview/ The viewer is self-unpacking and self-installing. Input files to be used alignment length (e.g. including gap characters). Also shown are with ETV (extension .etvx) can be found in the attachment to the some percent identities. A percent pairwise alignment identity is defi- main report. ned as (idents / MIN(len1, len2)) where idents is the number of 4.5 Citing this work exact identities and len1, len2 are the unaligned lengths of the two The method used to rank residues and make predictions in this report sequences. The ”average percent identity”, ”most related pair”, and can be found in Mihalek, I., I. Res,ˇ O. Lichtarge. (2004). ”A Family of ”most unrelated pair” of the alignment are the average, maximum, Evolution-Entropy Hybrid Methods for Ranking of Protein Residues and minimum of all (N)(N-1)/2 pairs, respectively. The ”most distant by Importance” J. Mol. Bio. 336: 1265-82. For the original version seq” is calculated by finding the maximum pairwise identity (best of ET see O. Lichtarge, H.Bourne and F. Cohen (1996). ”An Evolu- relative) for all N sequences, then finding the minimum of these N tionary Trace Method Defines Binding Surfaces Common to Protein numbers (hence, the most outlying sequence). alistat is copyrighted Families” J. Mol. Bio. 257: 342-358. by HHMI/Washington University School of Medicine, 1992-2001, report maker itself is described in Mihalek I., I. Res and O. and freely distributed under the GNU General Public License. Lichtarge (2006). ”Evolutionary Trace Report Maker: a new type 4.3.2 CE To map ligand binding sites from different of service for comparative analysis of proteins.” Bioinformatics source structures, report maker uses the CE program: 22:1656-7. http://cl.sdsc.edu/. Shindyalov IN, Bourne PE (1998) 4.6 About report maker ”Protein structure alignment by incremental combinatorial extension (CE) of the optimal path . Protein Engineering 11(9) 739-747. report maker was written in 2006 by Ivana Mihalek. The 1D ran- king visualization program was written by Ivica Res.ˇ report maker 4.3.3 DSSP In this work a residue is considered solvent accessi- 2 is copyrighted by Lichtarge Lab, Baylor College of Medicine, ble if the DSSP program finds it exposed to water by at least 10A˚ , Houston. which is roughly the area needed for one water molecule to come in the contact with the residue. DSSP is copyrighted by W. Kabsch, C. 4.7 Attachments Sander and MPI-MF, 1983, 1985, 1988, 1994 1995, CMBI version The following files should accompany this report: by [email protected] November 18,2002, • 1ujmA.complex.pdb - coordinates of 1ujmA with all of its http://www.cmbi.kun.nl/gv/dssp/descrip.html. interacting partners 4.3.4 HSSP Whenever available, report maker uses HSSP ali- • 1ujmA.etvx - ET viewer input file for 1ujmA gnment as a starting point for the analysis (sequences shorter than • 1ujmA.cluster report.summary - Cluster report summary for 75% of the query are taken out, however); R. Schneider, A. de 1ujmA Daruvar, and C. Sander. ”The HSSP database of protein structure- • 1ujmA.ranks - Ranks file in sequence order for 1ujmA sequence alignments.” Nucleic Acids Res., 25:226–230, 1997. • 1ujmA.clusters - Cluster descriptions for 1ujmA http://swift.cmbi.kun.nl/swift/hssp/ • 1ujmA.msf - the multiple sequence alignment used for the chain 1ujmA 4.3.5 LaTex The text for this report was processed using LATEX; Leslie Lamport, “LaTeX: A Document Preparation System Addison- • 1ujmA.descr - description of sequences used in 1ujmA msf Wesley,” Reading, Mass. (1986). • 1ujmA.ranks sorted - full listing of residues and their ranking 4.3.6 Muscle When making alignments “from scratch”, report for 1ujmA maker uses Muscle alignment program: Edgar, Robert C. (2004), • 1ujmA.1ujmSO41009.if.pml - Pymol script for Figure 5

8 • 1ujmA.cbcvg - used by other 1ujmA – related pymol scripts • 1ujmA.1ujmSO41003.if.pml - Pymol script for Figure 9 • 1ujmA.1ujmSO41004.if.pml - Pymol script for Figure 6 • 1ujmA.1ujmB.if.pml - Pymol script for Figure 10 • 1ujmA.1ujmSO41001.if.pml - Pymol script for Figure 7 • 1ujmA.1ujmSO41002.if.pml - Pymol script for Figure 8

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