Pages 1–8 2ux8 Evolutionary trace report by report maker January 2, 2010

4.3.3 DSSP 7 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 2ux8): Title: Crystal structure of sphingomonas elodea atcc 31461 glucose- 1-phosphate uridylyltransferase in complex with glucose-1- phos- phate. Compound: Mol id: 1; molecule: glucose-1-phosphate uridylyl- transferase; chain: a, b, c, d, e, f, g, h; ec: 2.7.7.9; engineered: yes; CONTENTS other details: co-crystallised with glucose-1-phosphate Organism, scientific name: Sphingomonas Elodea; 1 Introduction 1 2ux8 contains a single unique chain 2ux8G (288 residues long) and its homologues 2ux8F, 2ux8A, 2ux8E, 2ux8B, 2ux8H, 2ux8C, 2 Chain 2ux8G 1 and 2ux8D. 2.1 Q8RTG2 overview 1 2.2 Multiple sequence alignment for 2ux8G 1 2.3 Residue ranking in 2ux8G 1 2.4 Top ranking residues in 2ux8G and their position on the structure 2 2 CHAIN 2UX8G 2.4.1 Clustering of residues at 25% coverage. 2 2.4.2 Overlap with known functional surfaces at 2.1 Q8RTG2 overview 25% coverage. 2 From SwissProt, id Q8RTG2, 100% identical to 2ux8G: Description: UDP glucose pyrophosphorylase. 3 Notes on using trace results 6 Organism, scientific name: Pseudomonas paucimobilis (Sphingo- 3.1 Coverage 6 monas paucimobilis). 3.2 Known substitutions 6 Taxonomy: Bacteria; Proteobacteria; Alphaproteobacteria; Sphingo- 3.3 Surface 6 monadales; Sphingomonadaceae; Sphingomonas. 3.4 Number of contacts 7 3.5 Annotation 7 3.6 Mutation suggestions 7 2.2 Multiple sequence alignment for 2ux8G 4 Appendix 7 For the chain 2ux8G, the alignment 2ux8G.msf (attached) with 746 4.1 File formats 7 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 7 database, and fragments shorter than 75% of the query as well as 4.3 Credits 7 duplicate sequences were removed. It can be found in the attachment 4.3.1 Alistat 7 to this report, under the name of 2ux8G.msf. Its statistics, from the 4.3.2 CE 7 alistat program are the following:

1 Lichtarge lab 2006 Fig. 1. Residues 2-145 in 2ux8G colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.)

Fig. 2. Residues 146-289 in 2ux8G colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.)

Fig. 3. Residues in 2ux8G, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 746 Total number of residues: 204308 Smallest: 66 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 288 Average length: 273.9 Alignment length: 288 Average identity: 45% Most related pair: 99% Most unrelated pair: 0% Most distant seq: 35%

Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 23% prokaryotic, and 1% archaean sequences. (Descriptions of some sequences were not readily availa- ble.) The file containing the sequence descriptions can be found in the attachment, under the name 2ux8G.descr. 2.3 Residue ranking in 2ux8G The 2ux8G sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 2ux8G can be found in the file called 2ux8G.ranks sorted in the attachment. 2.4 Top ranking residues in 2ux8G and their position on the structure In the following we consider residues ranking among top 25% of Fig. 4. Residues in 2ux8G, colored according to the cluster they belong to: residues in the protein . Figure 3 shows residues in 2ux8G colored red, followed by blue and yellow are the largest clusters (see Appendix for by their importance: bright red and yellow indicate more conser- the coloring scheme). Clockwise: front, back, top and bottom views. The ved/important residues (see Appendix for the coloring scheme). A corresponding Pymol script is attached. Pymol script for producing this figure can be found in the attachment. in Table 1. 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the top 25% of all residues, this time colored according to clusters they

2 Table 1. Table 3. continued cluster size member res type disruptive color residues mutations red 63 8,12,14,15,17,18,19,20,21,22 113 H (E)(M)(Q)(TD) 23,24,25,28,29,30,31,32,33 60 G (R)(K)(E)(FWH) 35,38,46,47,51,60,63,105,110 111,112,113,114,118,127,129 Table 3. List of disruptive mutations for the top 25% of residues in 131,132,133,134,171,172,191 2ux8G, that are at the interface with 2ux8H. 192,193,206,207,208,210,215 218,224,226,228,230,231,232 233,253,255,256,257,261,265 blue 3 76,77,80 yellow 2 198,200

Table 1. Clusters of top ranking residues in 2ux8G.

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. Interface with 2ux8H.Table 2 lists the top 25% of residues at the interface with 2ux8H. 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˚ ) 105 Q Q(99).P 0.02 6/6 3.76 E 70 F F(93)Y 0.11 2/2 4.41 L(2)T .(1)IWV RA 113 H H(82) 0.19 4/0 4.58 Fig. 5. Residues in 2ux8G, at the interface with 2ux8H, colored by their rela- D(15)ER tive importance. 2ux8H is shown in backbone representation (See Appendix N(1).YS for the coloring scheme for the protein chain 2ux8G.) TQG 60 G G(65) 0.24 2/2 4.79 A(2) Figure 5 shows residues in 2ux8G colored by their importance, at the S(11) interface with 2ux8H. H(14) G1P binding site. By analogy with 2ux8A – 2ux8AG1P1290 N(2)PD. interface. Table 4 lists the top 25% of residues at the interface ERT with 2ux8AG1P1290 (g1p). The following table (Table 5) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. The top 25% of residues in 2ux8G at the interface with 2ux8H. Table 4. (Field names: res: residue number in the PDB entry; type: amino acid type; res type subst’s cvg noc/ dist antn substs: substitutions seen in the alignment; with the percentage of each type (%) bb (A˚ ) in the bracket; noc/bb: number of contacts with the ligand, with the number of 192 K K(99)N. 0.01 2/0 3.66 contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) 208 Y Y(98)FC 0.02 8/0 3.02 site .V 133 D D(99)SG 0.03 2/0 4.60 Table 3. . res type disruptive 131 L L(95)A 0.04 14/0 3.20 mutations V(1)I 105 Q (Y)(H)(FTW)(CG) N(1)F 70 F (K)(E)(Q)(D) Y(1)TW. continued in next column continued in next column

3 Table 4. continued Table 5. continued res type subst’s cvg noc/ dist antn res type disruptive (%) bb (A˚ ) mutations 206 G G(98)SP 0.04 8/8 3.99 204 V (R)(Y)(K)(E) .A 255 D D(97) 0.04 2/0 4.63 Table 5. List of disruptive mutations for the top 25% of residues in .(1)NMR 2ux8G, that are at the interface with G1P. 111 L L(95) 0.06 8/1 3.97 site T(2)FN. IPYV 171 Y Y(91) 0.12 5/0 3.81 site V(2) S(2) F(2)HTA .IW 134 D D(65) 0.18 15/0 3.64 N(3) M(5) T(3) V(15) E(3)S I(1)HY. 253 R R(68) 0.20 1/0 4.59 W(5) T(7)I S(12) .(1)MNH LYACGV 204 V V(35) 0.25 10/8 2.82 I(49) N(1) A(8) L(2)TC Fig. 6. Residues in 2ux8G, at the interface with G1P, colored by their relative S(1)M. importance. The ligand (G1P) 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 Table 4. The top 25% of residues in 2ux8G at the interface with chain 2ux8G.) G1P.(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- Figure 6 shows residues in 2ux8G colored by their importance, at the ber of contacts realized through backbone atoms given in the bracket; dist: interface with 2ux8AG1P1290. distance of closest apporach to the ligand. ) G1P binding site. Table 6 lists the top 25% of residues at the interface with 2ux8GG1P1290 (g1p). The following table (Table Table 5. 7) suggests possible disruptive replacements for these residues (see Section 3.6). res type disruptive mutations Table 6. 192 K (Y)(FTW)(VCAG)(S) res type subst’s cvg noc/ dist antn 208 Y (K)(Q)(M)(E) (%) bb (A˚ ) 133 D (R)(FWH)(K)(Y) 191 E E(99). 0.00 18/1 2.51 131 L (R)(Y)(K)(H) 192 K K(99)N. 0.01 1/0 4.44 206 G (R)(K)(E)(H) 208 Y Y(98)FC 0.02 11/0 3.36 site 255 D (R)(FWH)(Y)(CG) .V 111 L (R)(Y)(H)(K) 131 L L(95)A 0.04 7/0 4.12 171 Y (K)(Q)(E)(M) V(1)I 134 D (R)(H)(FW)(K) N(1)F 253 R (D)(E)(T)(Y) Y(1)TW. continued in next column continued in next column

4 Table 6. continued res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 232 T T(97)SI 0.04 9/1 3.30 site V.A 111 L L(95) 0.06 12/0 2.95 site T(2)FN. IPYV 172 G G(93) 0.09 14/14 3.07 site A(2) V(1) S(1)EC. F 171 Y Y(91) 0.12 17/8 2.85 site V(2) S(2) F(2)HTA .IW 231 L L(85) 0.12 2/0 4.70 V(1) I(12)HF . 204 V V(35) 0.25 22/12 2.73 Fig. 7. Residues in 2ux8G, at the interface with G1P, colored by their relative I(49) importance. The ligand (G1P) is colored green. Atoms further than 30A˚ away N(1) from the geometric center of the ligand, as well as on the line of sight to the A(8) ligand were removed. (See Appendix for the coloring scheme for the protein L(2)TC chain 2ux8G.) S(1)M.

Table 6. The top 25% of residues in 2ux8G at the interface with G1P.(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 191 E (FWH)(VCAG)(YR)(T) 192 K (Y)(FTW)(VCAG)(S) 208 Y (K)(Q)(M)(E) 131 L (R)(Y)(K)(H) 232 T (R)(K)(H)(Q) 111 L (R)(Y)(H)(K) 172 G (KR)(E)(QH)(D) 171 Y (K)(Q)(E)(M) 231 L (R)(Y)(T)(E) 204 V (R)(Y)(K)(E)

Table 7. List of disruptive mutations for the top 25% of residues in 2ux8G, that are at the interface with G1P.

Figure 7 shows residues in 2ux8G colored by their importance, at the interface with 2ux8GG1P1290. Interface with 2ux8F.Table 8 lists the top 25% of residues at the interface with 2ux8F. The following table (Table 9) suggests possible disruptive replacements for these residues (see Section 3.6).

5 Table 8. Table 8. continued res type subst’s cvg noc/ dist res type subst’s cvg noc/ dist (%) bb (A˚ ) (%) bb (A˚ ) 38 P P(97) 0.05 11/3 3.86 80 M L(81)V 0.22 4/0 3.90 .(2)AR I(9) 22 P P(96) 0.07 50/17 3.12 F(2) .(3)E .(3)MAN 70 F F(93)Y 0.11 3/3 4.25 CKPYQ L(2)T 35 V V(75)F 0.24 21/13 3.75 .(1)IWV L(5) RA A(6) 21 L L(89)V 0.13 27/12 3.32 G(1) R(4) I(5) .(3)GYS .(2)PTN HFE MY(1) 33 P P(80) 0.14 14/1 3.85 77 E E(87)VA 0.24 2/0 4.45 T(13)I D(3) N(2) K(1)G .(2)SDQ Y(1) YR .(1)QNC 31 M M(81) 0.15 13/5 2.85 SIRTF I(4) 76 L L(87)F 0.25 20/3 3.79 L(10) I(6)PG .(2)VSF .(1) A V(1)HWK 32 L L(84) 0.15 7/1 3.69 XATY M(6) F(1) Table 8. The top 25% of residues in 2ux8G at the interface with 2ux8F. I(1) (Field names: res: residue number in the PDB entry; type: amino acid type; V(2) substs: substitutions seen in the alignment; with the percentage of each type .(2) in the bracket; noc/bb: number of contacts with the ligand, with the number of 18 T T(90) 0.18 8/0 3.46 contacts realized through backbone atoms given in the bracket; dist: distance S(2) of closest apporach to the ligand. ) M(2) .(3)VK 20 F F(69) 0.19 6/4 3.62 Table 9. L(8) res type disruptive M(14)NC mutations V(3)S 38 P (Y)(TR)(H)(E) .(3) 22 P (YR)(H)(T)(CG) 25 K K(90) 0.20 66/4 2.73 70 F (K)(E)(Q)(D) Y(1) 21 L (R)(Y)(K)(T) F(1) 33 P (R)(Y)(H)(T) .(3)ENR 31 M (Y)(H)(R)(T) DHSL 32 L (YR)(T)(H)(KE) 23 A A(82)Y 0.22 24/14 2.79 18 T (R)(H)(K)(FW) I(5) 20 F (KE)(DR)(TQ)(SNCG) H(1) 25 K (Y)(T)(FW)(CG) V(1) 23 A (R)(KE)(Y)(D) L(3) 80 M (Y)(H)(T)(R) .(3)TFQ 35 V (R)(K)(E)(Y) GM 77 E (H)(FW)(R)(Y) 76 L (R)(Y)(E)(TK) continued in next column

Table 9. List of disruptive mutations for the top 25% of residues in 2ux8G, that are at the interface with 2ux8F.

Figure 8 shows residues in 2ux8G colored by their importance, at the interface with 2ux8F.

6 2 at least 10A˚ , which is roughly the area needed for one water mole- cule to come in the contact with the residue. Furthermore, we require that these residues form a “cluster” of residues which have neighbor within 5A˚ from any of their heavy atoms. Note, however, that, if our picture of protein evolution is correct, the neighboring residues which are not surface accessible might be equally important in maintaining the interaction specificity - they should not be automatically dropped from consideration when choo- sing the set for mutagenesis. (Especially if they form a cluster with the surface residues.) 3.4 Number of contacts Another column worth noting is denoted “noc/bb”; it tells the num- ber of contacts heavy atoms of the residue in question make across the interface, as well as how many of them are realized through the backbone atoms (if all or most contacts are through the backbone, mutation presumably won’t have strong impact). Two heavy atoms are considered to be “in contact” if their centers are closer than 5A˚ . 3.5 Annotation If the residue annotation is available (either from the pdb file or from other sources), another column, with the header “annotation” Fig. 8. Residues in 2ux8G, at the interface with 2ux8F, colored by their rela- appears. Annotations carried over from PDB are the following: site tive importance. 2ux8F is shown in backbone representation (See Appendix (indicating existence of related site record in PDB ), S-S (disulfide for the coloring scheme for the protein chain 2ux8G.) bond forming residue), hb (hydrogen bond forming residue, jb (james bond forming residue), and sb (for salt bridge forming residue). 3.6 Mutation suggestions 3 NOTES ON USING TRACE RESULTS Mutation suggestions are completely heuristic and based on comple- 3.1 Coverage mentarity with the substitutions found in the alignment. Note that Trace results are commonly expressed in terms of coverage: the resi- they are meant to be disruptive to the interaction of the protein due is important if its “coverage” is small - that is if it belongs to with its ligand. The attempt is made to complement the following some small top percentage of residues [100% is all of the residues properties: small [AV GSTC], medium [LPNQDEMIK], large in a chain], according to trace. The ET results are presented in the [WFYHR], hydrophobic [LPVAMWFI], polar [GTCY ]; posi- form of a table, usually limited to top 25% percent of residues (or tively [KHR], or negatively [DE] charged, aromatic [WFYH], to some nearby percentage), sorted by the strength of the presumed long aliphatic chain [EKRQM], OH-group possession [SDETY ], evolutionary pressure. (I.e., the smaller the coverage, the stronger the and NH2 group possession [NQRK]. The suggestions are listed pressure on the residue.) Starting from the top of that list, mutating a according to how different they appear to be from the original amino couple of residues should affect the protein somehow, with the exact acid, and they are grouped in round brackets if they appear equally effects to be determined experimentally. disruptive. From left to right, each bracketed group of amino acid types resembles more strongly the original (i.e. is, presumably, less 3.2 Known substitutions 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- 4.1 File formats sely, when looking for substitutions which will not affect the protein, Files with extension “ranks sorted” are the actual trace results. The one may try replacing, R with K, or (perhaps more surprisingly), with fields in the table in this file: V. The percentage of times the substitution appears in the alignment is given in the immediately following bracket. No percentage is given • alignment# number of the position in the alignment in the cases when it is smaller than 1%. This is meant to be a rough • residue# residue number in the PDB file guide - due to rounding errors these percentages often do not add up • to 100%. type amino acid type • rank rank of the position according to older version of ET 3.3 Surface • variability has two subfields: To detect candidates for novel functional interfaces, first we look for 1. number of different amino acids appearing in in this column residues that are solvent accessible (according to DSSP program) by of the alignment

7 4.3.2 CE To map ligand binding sites from different source structures, report maker uses the CE program: http://cl.sdsc.edu/. Shindyalov IN, Bourne PE (1998) ”Protein structure alignment by incremental combinatorial extension COVERAGE (CE) of the optimal path . Protein Engineering 11(9) 739-747. 4.3.3 DSSP In this work a residue is considered solvent accessi- V ble if the DSSP program finds it exposed to water by at least 10A˚ 2, 100% 50% 30% 5% 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. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995, CMBI version by [email protected] November 18,2002, http://www.cmbi.kun.nl/gv/dssp/descrip.html. V

RELATIVE IMPORTANCE 4.3.4 HSSP Whenever available, report maker uses HSSP ali- gnment as a starting point for the analysis (sequences shorter than 75% of the query are taken out, however); R. Schneider, A. de Fig. 9. Coloring scheme used to color residues by their relative importance. Daruvar, and C. Sander. ”The HSSP database of protein structure- sequence alignments.” Nucleic Acids Res., 25:226–230, 1997. http://swift.cmbi.kun.nl/swift/hssp/ 2. their type 4.3.5 LaTex The text for this report was processed using LAT X; • rho ET score - the smaller this value, the lesser variability of E Leslie Lamport, “LaTeX: A Document Preparation System Addison- this position across the branches of the tree (and, presumably, Wesley,” Reading, Mass. (1986). the greater the importance for the protein) • cvg coverage - percentage of the residues on the structure which 4.3.6 Muscle When making alignments “from scratch”, report have this rho or smaller maker uses Muscle alignment program: Edgar, Robert C. (2004), ”MUSCLE: multiple sequence alignment with high accuracy and • gaps percentage of gaps in this column high throughput.” Nucleic Acids Research 32(5), 1792-97. 4.2 Color schemes used http://www.drive5.com/muscle/ The following color scheme is used in figures with residues colored 4.3.7 Pymol The figures in this report were produced using by cluster size: black is a single-residue cluster; clusters composed of Pymol. The scripts can be found in the attachment. Pymol more than one residue colored according to this hierarchy (ordered is an open-source application copyrighted by DeLano Scien- by descending size): red, blue, yellow, green, purple, azure, tur- tific LLC (2005). For more information about Pymol see quoise, brown, coral, magenta, LightSalmon, SkyBlue, violet, gold, http://pymol.sourceforge.net/. (Note for Windows bisque, LightSlateBlue, orchid, RosyBrown, MediumAquamarine, users: the attached package needs to be unzipped for Pymol to read DarkOliveGreen, CornflowerBlue, grey55, burlywood, LimeGreen, the scripts and launch the viewer.) tan, DarkOrange, DeepPink, maroon, BlanchedAlmond. The colors used to distinguish the residues by the estimated 4.4 Note about ET Viewer evolutionary pressure they experience can be seen in Fig. 9. Dan Morgan from the Lichtarge lab has developed a visualization tool specifically for viewing trace results. If you are interested, please 4.3 Credits visit: 4.3.1 Alistat alistat reads a multiple sequence alignment from the http://mammoth.bcm.tmc.edu/traceview/ file and shows a number of simple statistics about it. These stati- stics include the format, the number of sequences, the total number The viewer is self-unpacking and self-installing. Input files to be used of residues, the average and range of the sequence lengths, and the with ETV (extension .etvx) can be found in the attachment to the alignment length (e.g. including gap characters). Also shown are main report. some percent identities. A percent pairwise alignment identity is defi- 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

8 of service for comparative analysis of proteins.” Bioinformatics • 2ux8G.ranks - Ranks file in sequence order for 2ux8G 22:1656-7. • 2ux8G.clusters - Cluster descriptions for 2ux8G 4.6 About report maker • 2ux8G.msf - the multiple sequence alignment used for the chain report maker was written in 2006 by Ivana Mihalek. The 1D ran- 2ux8G king visualization program was written by Ivica Res.ˇ report maker • 2ux8G.descr - description of sequences used in 2ux8G msf is copyrighted by Lichtarge Lab, Baylor College of Medicine, • 2ux8G.ranks sorted - full listing of residues and their ranking Houston. for 2ux8G 4.7 Attachments • 2ux8G.2ux8H.if.pml - Pymol script for Figure 5 The following files should accompany this report: • 2ux8G.cbcvg - used by other 2ux8G – related pymol scripts • • 2ux8G.complex.pdb - coordinates of 2ux8G with all of its 2ux8G.2ux8AG1P1290.if.pml - Pymol script for Figure 6 interacting partners • 2ux8G.2ux8GG1P1290.if.pml - Pymol script for Figure 7 • 2ux8G.etvx - ET viewer input file for 2ux8G • 2ux8G.2ux8F.if.pml - Pymol script for Figure 8 • 2ux8G.cluster report.summary - Cluster report summary for 2ux8G

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