Group:SMART:2010 Pingry SMART Team Models

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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 mutant

Design 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 testosterone

Model 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]