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Group:SMART:2010 Pingry SMART Team Models

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'''Return to 2010 SMART Team Page:''' [[2010 Pingry SMART Team]]
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<StructureSection load='AdhD_with_three_cofactors_no_H.pdb' size='450' side='right' scene='2010_Pingry_SMART_Team/Adhd_final_default/2' caption=''>
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'''Return to 2010 SMART Team Page:''' [[Group:SMART:2010 Pingry SMART Team | 2010 Pingry SMART Team]]
{{Clear}}
{{Clear}}
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Sheet color (red): [255,128,128]
Sheet color (red): [255,128,128]
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Three residues (ARG-R, SER-S, ASN-N; residue numbers differ by structure) that bind cofactor:
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Three residues (ARG-R, SER-S, ASN-N; residue numbers differ by structure) that bind cofactor: display sidechains and color CPK
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Display sidechains and color CPK
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== AdhD K249G/H255R double mutant ==
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== AdhD K249G/H255R double mutant and Self-assembly into hydrogels ==
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'''Design description'''
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<applet load='AdhD_with_three_cofactors_no_H.pdb' size='400' frame='true' align='right' caption='AdhD K249G/H255R double mutant' scene='2010_Pingry_SMART_Team/Adhd_0/2'/>
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 +
(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.
 +
 
 +
<scene name='2010_Pingry_SMART_Team/Adhd_final_default_nad/2'>Show NAD</scene>
 +
 
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<scene name='2010_Pingry_SMART_Team/Adhd_final_default_nadp/1'>Show NADP</scene>
 +
 
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<scene name='2010_Pingry_SMART_Team/Adhd_final_default_nmn/1'>Show nicotimanide</scene>
 +
 
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<scene name='2010_Pingry_SMART_Team/Adhd_final_default/2'>Return to default</scene>
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(β/α)<sub>8</sub> secondary structure features colored blue and red.
 
'''Design script:'''
'''Design script:'''
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Color cpk
Color cpk
 +
 +
Select 5
 +
 +
Color [0,0,128]
 +
 +
Select 276
 +
 +
Color [128,0,0]
{{Clear}}
{{Clear}}
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==PDB ID: 1a80, 2,5-diketo-d-gluconic acid reductase with NADPH (wild-type)==
 
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<applet load='1a80' size='400' frame='true' align='right' caption='1a80, 2,5-diketo-d-gluconic acid reductase with NADPH (wild-type)' scene='2010_Pingry_SMART_Team/1a80-original/22'/>
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==PDB ID: [[1m9h]], Mutant 2,5-diketo-d-gluconic acid reductase with NADH (mutant)==
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<scene name='2010_Pingry_SMART_Team_Models/1m9h_final/3'>Mutant 2,5-diketo-d-gluconic acid reductase with NADH</scene>
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'''Design description'''
 +
(β/α)8 secondary structure features colored blue and red.
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Four mutated residues have backbone colored orange: F22Y, K232G, R238H, A272G
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{{Clear}}
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Other residues involved in cofactor binding: S233, V234, W187
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==PDB ID: 1m9h, Mutant 2,5-diketo-d-gluconic acid reductase with NADH (mutant)==
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Amino terminus colored dark blue: [0,0,128]
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<applet load='1m9h' size='400' frame='true' align='right' caption='1m9h, Mutant 2,5-diketo-d-gluconic acid reductase with NADH' scene='2010_Pingry_SMART_Team/1m9h_default/1'/>
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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
 +
 
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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]
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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)
Select (22 or 232 or 238 or 272) and (sidechain or alpha)
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Wireframe 250
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 +
Wireframe 300
 +
 
Select (22 or 232 or 238 or 272) and sidechain
Select (22 or 232 or 238 or 272) and sidechain
 +
Color cpk
Color cpk
 +
Select (22 or 232 or 238 or 272) and alpha
Select (22 or 232 or 238 or 272) and alpha
 +
Color [255,128,0]
Color [255,128,0]
Select (233 or 234) and (sidechain or alpha)
Select (233 or 234) and (sidechain or alpha)
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Wireframe 250
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 +
Wireframe 300
 +
 
Select (233 or 234) and sidechain
Select (233 or 234) and sidechain
 +
Color CPK
Color CPK
Select 187 and (sidechain or alpha)
Select 187 and (sidechain or alpha)
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Wireframe 250
+
 
 +
Wireframe 300
 +
 
Select 187 and sidechain
Select 187 and sidechain
 +
Color CPK
Color CPK
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Display sidechain
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Select 2
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Color sidechain CPK
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 +
Color [0,0,128]
 +
 
 +
Select 278
 +
 
 +
Color [128,0,0]
{{Clear}}
{{Clear}}
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==PDB ID: 1mi3, Xylose reductase with NAD+==
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==PDB ID: [[1mi3]], Xylose reductase with NAD+==
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<scene name='2010_Pingry_SMART_Team_Models/1mi3_final/7'>Xylose reductase with NAD+</scene>
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<applet load='1MI3_chainA.pdb' size='400' frame='true' align='right' caption='1mi3, Xylose reductase with NAD+' scene='2010_Pingry_SMART_Team_Models/1mi3_model/1'/>
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Select all
 
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Cartoon off
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'''Design description'''
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Spacefill off
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(β/α)8 secondary structure features colored blue and red.
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Backbone 300
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Three residues involved in NAD+ binding have backbones colored green: E227, N276, R280.
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Color white
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Two additional residues involved in NADP+ binding but not NAD+ binding have sidechains displayed but backbone uncolored: K274 or S275.
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Select hetero and not water
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Other residues involved in cofactor binding: S233, V234, W187, Y217
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Wireframe 250
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Loops that make a conformational change to bind NAD+ or NADP+ colored yellow.
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Color cpk
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Amino terminus colored dark blue: [0,0,128].
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Select 27-41 or 54-68 or 89-104 or 146-160 or 172-183 or 200-210 or 255-266 or 277-286
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Carboxyl terminus colored cherry: [128,0,0].
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Color [128,255,255]
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NAD+ shown in wireframe.
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Select 20-22 or 45-47 or 77-82 or 108-113 or 163-169 or 189-193 or 213-217 or 270-271
 
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Color [255,128,128]
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'''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
Select 274-280
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Color [255,255,0]
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Color [255,255,0]
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Select 225-229
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Select 225-229
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Color [255,128,0]
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Color [255,255,0]
-
select (275 or 276 or 280) and (sidechain or alpha)
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select (227 or 276 or 280) and (sidechain or alpha)
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wireframe 250
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wireframe 250
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select (275 or 276 or 280) and (sidechain)
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select (227 or 276 or 280) and (sidechain)
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color cpk
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color cpk
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select (275 or 276 or 280) and (alpha)
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select (227 or 276 or 280) and (alpha)
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color [128,128,255]
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color [255,128,0]
-
select (274 or 227) and (sidechain or alpha)
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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
wireframe 250
-
select (274 or 227) and (sidechain)
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select 217 and sidechain
color cpk
color cpk
 +
 +
Select 4
 +
 +
Color [0,0,128]
 +
 +
Select 322
 +
 +
Color [128,0,0]
{{Clear}}
{{Clear}}
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==PDB ID: 1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone==
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==PDB ID: [[1afs]], Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone==
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<scene name='2010_Pingry_SMART_Team_Models/1afs_final2/1'>Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone</scene>
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'''Model description'''
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<applet load='1AFS_chainA.pdb' size='400' frame='true' align='right' caption='1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone' scene='2010_Pingry_SMART_Team/1afs_default/7'/>
 
 +
'''Model script'''
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select all
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select all
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backbone off
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backbone off
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spacefill off
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spacefill off
-
cartoon off
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cartoon off
-
wireframe off
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wireframe off
-
backbone 300
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backbone 350
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color white
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color white
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select hetero and not water
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select tes or nap
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wireframe 250
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wireframe 250
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color cpk
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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)
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select sheet
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color [255,128,128]
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color [255, 128, 128]
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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)
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select 274-284 or 253-263 or 200-209 or 170-177 or 145-156 or 92-106 or 58-70 or 31-43
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wireframe 250
-
color [128, 255, 255]
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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)
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select (54 or 86 or 118 or 120 or 122 or 128 or 129 or 137 or 139 or 227) and (sidechain)
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wireframe 250
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wireframe 250
+
select (50 or 55 or 84) and (sidechain)
-
color cpk
+
color [128,0,128]
-
select (50 or 55 or 84) and (sidechain)
+
select (28 or 224) and (sidechain or alpha)
-
wireframe 250
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wireframe 250
-
color [128,0,128]
+
select (28 or 224) and (sidechain)
-
select (28 or 224) and (sidechain)
+
color [0,128,0]
-
wireframe 250
+
select (276 or 271 or 273 or 216) and (sidechain or alpha)
-
color [0,255,0]
+
wireframe 250
-
select (24 or 166 or 167 or 190 or 216 or 219 or 221 or 270 or 271 or 272 or 276) and (sidechain)
+
select (276 or 273 or 271 or 216) and (sidechain)
-
wireframe 250
+
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
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color [255,127,0]
+
color [0,0,255]
-
select 116-142 and backbone
+
select 217-235 and backbone
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color [0,0,255]
+
color [0,0,255]
-
select 217-235 and backbone
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Select 1
-
color [0,0,255]
+
Color [0,0,128]
 +
Select 319
-
+
Color [128,0,0]
{{Clear}}
{{Clear}}

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