Group:SMART:2010 Pingry SMART Team Models
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Return to 2010 SMART Team Page: 2010 Pingry SMART Team General design guidelines Helix color (blue): [128,128,192] Sheet color (red): [255,128,128] Three residues (ARG-R, SER-S, ASN-N; residue numbers differ by structure) that bind cofactor: display sidechains and color CPK
AdhD K249G/H255R double mutantDesign description (β/α)8 secondary structure features colored blue and red. Two mutated residues have backbone colored blue: K249G and H255R Residues involved in cofactor binding and commonly seen in AKR's have sidechains highlighted: S251, N252, and H255R.
Design script: Select all Backbone off Wireframe off Spacefill off Cartoon off Backbone 300 Color white Select (253-260) or (230-241) or (190-198) or (157-165) or (131-144) or (98-112) or (68-78) or (40-53) Color [128,128,192] Select (118-122) or (149-153) or (174-177) or (201-205) or (244-249) or (22-25) or (57-61) or (86-91) Color [255,128,128] Select 249 and (sidechain or alpha) Wireframe 250 Select 249 and sidechain Color cpk Select 249 and alpha Color [0,0,255] Select 255 and (sidechain or alpha) Wireframe 250 Select 255 and sidechain Color cpk Select 255 and alpha Color [0,0,255] Select (251 or 252) and (sidechain or alpha) Wireframe 250 Select (251 or 252) and (sidechain) Color cpk Select 5 Color [0,0,128] Select 276 Color [128,0,0] PDB ID: 1m9h, Mutant 2,5-diketo-d-gluconic acid reductase with NADH (mutant)
Design description (β/α)8 secondary structure features colored blue and red. Four mutated residues have backbone colored orange: F22Y, K232G, R238H, A272G Other residues involved in cofactor binding: S233, V234, W187 Amino terminus colored dark blue: [0,0,128] Carboxyl terminus colored cherry: [128,0,0] NADH shown in wireframe
Design script Select all Backbone off Wireframe off Spacefill off Select *a Color white Backbone 350 Select nad Wireframe 300 Color cpk Select (142-154) or (170-181) or (117-130) or (84-98) or (48-63) or (26-39) or (236-246) or (214-225) Color [128,128,192] Select (18-21) or (43-45) or (71-76) or (102-107) or (133-139) or (159-163) or (183-187) or (228-231) Color [255,128,128] Select (22 or 232 or 238 or 272) and (sidechain or alpha) Wireframe 300 Select (22 or 232 or 238 or 272) and sidechain Color cpk Select (22 or 232 or 238 or 272) and alpha Color [255,128,0] Select (233 or 234) and (sidechain or alpha) Wireframe 300 Select (233 or 234) and sidechain Color CPK Select 187 and (sidechain or alpha) Wireframe 300 Select 187 and sidechain Color CPK Select 2 Color [0,0,128] Select 278 Color [128,0,0] PDB ID: 1mi3, Xylose reductase with NAD+
Design description (β/α)8 secondary structure features colored blue and red. Three residues involved in NAD+ binding have backbones colored green: E227, N276, R280. Two additional residues involved in NADP+ binding but not NAD+ binding have sidechains displayed but backbone uncolored: K274 or S275. Other residues involved in cofactor binding: S233, V234, W187, Y217 Loops that make a conformational change to bind NAD+ or NADP+ colored yellow. Amino terminus colored dark blue: [0,0,128]. Carboxyl terminus colored cherry: [128,0,0]. NAD+ shown in wireframe.
Design script Select all Cartoon off Spacefill off Backbone 350 Color white Select nad Wireframe 250 Color cpk Select 28-41 or 55-68 or 89-103 or 147-160 or 173-182 or 201-210 or 256-266 or 278-287 Color [128,128,192] Select 19-22 or 45-49 or 77-81 or 110-112 or 165-169 or 189-192 or 213-217 or 269-271 Color [255,128,128] Select 274-280 Color [255,255,0] Select 225-229 Color [255,255,0] select (227 or 276 or 280) and (sidechain or alpha) wireframe 250 select (227 or 276 or 280) and (sidechain) color cpk select (227 or 276 or 280) and (alpha) color [255,128,0] select (274 or 275) and (sidechain or alpha) wireframe 250 select (274 or 275) and (sidechain) color cpk select (217) and (sidechain or alpha) wireframe 250 select 217 and sidechain color cpk Select 4 Color [0,0,128] Select 322 Color [128,0,0] PDB ID: 1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosteroneModel description
Model script select all backbone off spacefill off cartoon off wireframe off backbone 350 color white select tes or nap wireframe 250 color cpk select sheet select (188-191) or (162-166) or (113-115) or (81-84) or (49-52) or (19-22) or (267-270) or (212-216) color [255,128,128] select 274-284 or 252-263 or 200-209 or 170-178 or 145-156 or 92-106 or 58-71 or 31-44 color [128, 128, 192] select (54 or 86 or 118 or 120 or 122 or 128 or 129 or 137 or 139 or 227) and (sidechain or alpha) wireframe 250 select (54 or 86 or 118 or 120 or 122 or 128 or 129 or 137 or 139 or 227) and (sidechain) color cpk select (50 or 55 or 84) and (sidechain or alpha) wireframe 250 select (50 or 55 or 84) and (sidechain) color [128,0,128] select (28 or 224) and (sidechain or alpha) wireframe 250 select (28 or 224) and (sidechain) color [0,128,0] select (276 or 271 or 273 or 216) and (sidechain or alpha) wireframe 250 select (276 or 273 or 271 or 216) and (sidechain) color cpk select (24 or 166 or 167 or 190 or 216 or 219 or 221 or 270 or 271 or 272 or 276 or 273) and (alpha) color [255,128,0] select 116-142 and backbone color [0,0,255] select 217-235 and backbone color [0,0,255] Select 1 Color [0,0,128] Select 319 Color [128,0,0]
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