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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.
Amino terminus colored dark blue: [0,0,128]
Carboxyl terminus colored cherry: [128,0,0]
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]
