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Group:SMART:2010 Pingry SMART Team Models

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(→PDB ID: 1a80, 2,5-diketo-d-gluconic acid reductase with NADPH (wild-type))
Current revision (11:53, 23 April 2013) (edit) (undo)
 
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'''Return to 2010 SMART Team Page:''' [[2010 Pingry SMART Team]]
+
<StructureSection load='AdhD_with_three_cofactors_no_H.pdb' size='450' side='right' scene='2010_Pingry_SMART_Team/Adhd_final_default/2' caption=''>
 +
'''Return to 2010 SMART Team Page:''' [[Group:SMART:2010 Pingry SMART Team | 2010 Pingry SMART Team]]
{{Clear}}
{{Clear}}
'''General design guidelines'''
'''General design guidelines'''
-
Helix color (blue): [128,255,255]
+
Helix color (blue): [128,128,192]
Sheet color (red): [255,128,128]
Sheet color (red): [255,128,128]
-
Three residues (ARG, SER, ASN; residue numbers differ by structure) that bind cofactor:
+
Three residues (ARG-R, SER-S, ASN-N; residue numbers differ by structure) that bind cofactor: display sidechains and color CPK
-
CPK the sidechain, color backbone (dark blue) [128,128,255]
+
== 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.
 +
 
 +
<scene name='2010_Pingry_SMART_Team/Adhd_final_default_nad/2'>Show NAD</scene>
 +
 
 +
<scene name='2010_Pingry_SMART_Team/Adhd_final_default_nadp/1'>Show NADP</scene>
 +
 
 +
<scene name='2010_Pingry_SMART_Team/Adhd_final_default_nmn/1'>Show nicotimanide</scene>
 +
 
 +
<scene name='2010_Pingry_SMART_Team/Adhd_final_default/2'>Return to default</scene>
-
== AdhD K249G/H255R double mutant and Self-assembly into hydrogels ==
 
-
<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'/>
 
'''Design script:'''
'''Design script:'''
-
Select all
+
Select all
-
Backbone off
+
Backbone off
-
Wireframe off
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Wireframe off
-
Spacefill off
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Spacefill off
-
Cartoon off
+
Cartoon off
-
Backbone 300
+
Backbone 300
-
Color white
+
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)
+
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 [128,255,255]
+
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)
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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]
+
Color [255,128,128]
-
Select 249 and (sidechain or alpha)
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Select 249 and (sidechain or alpha)
-
Wireframe 250
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Wireframe 250
-
Select 249 and sidechain
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Select 249 and sidechain
-
Color cpk
+
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 249 and alpha
+
Select 255 and alpha
-
Color [0,0,255]
+
Color [0,0,255]
-
Select 255 and (sidechain or alpha)
+
Select (251 or 252) and (sidechain or alpha)
Wireframe 250
Wireframe 250
-
Select 255 and sidechain
+
Select (251 or 252) and (sidechain)
Color cpk
Color cpk
-
Select 255 and alpha
+
Select 5
-
Color [0,0,255]
+
Color [0,0,128]
 +
 
 +
Select 276
 +
 
 +
Color [128,0,0]
{{Clear}}
{{Clear}}
-
 
-
==PDB ID: 1a80, 2,5-diketo-d-gluconic acid reductase with NADPH (wild-type)==
 
-
<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'/>
+
==PDB ID: [[1m9h]], Mutant 2,5-diketo-d-gluconic acid reductase with NADH (mutant)==
 +
<scene name='2010_Pingry_SMART_Team_Models/1m9h_final/3'>Mutant 2,5-diketo-d-gluconic acid reductase with NADH</scene>
 +
'''Design description'''
 +
(β/α)8 secondary structure features colored blue and red.
 +
Four mutated residues have backbone colored orange: F22Y, K232G, R238H, A272G
-
{{Clear}}
+
Other residues involved in cofactor binding: S233, V234, W187
-
==PDB ID: 1m9h, Mutant 2,5-diketo-d-gluconic acid reductase with NADH (mutant)==
+
Amino terminus colored dark blue: [0,0,128]
-
<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'/>
+
Carboxyl terminus colored cherry: [128,0,0]
-
{{Clear}}
+
NADH shown in wireframe
-
==PDB ID: 1mi3, Xylose reductase with NAD+==
+
 
-
+
'''Design script'''
-
<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'/>
+
Select all
Select all
-
Cartoon off
+
Backbone off
 +
 
 +
Wireframe off
Spacefill off
Spacefill off
-
Backbone 300
+
Select *a
Color white
Color white
-
Select hetero and not water
+
Backbone 350
-
Wireframe 250
+
Select nad
 +
 
 +
Wireframe 300
Color cpk
Color cpk
-
Select 27-41 or 54-68 or 89-104 or 146-160 or 172-183 or 200-210 or 255-266 or 277-286
+
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 [128,255,255]
+
Color [128,128,192]
-
Select 20-22 or 45-47 or 77-82 or 108-113 or 163-169 or 189-193 or 213-217 or 270-271
+
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]
+
Color [255,128,128]
-
Select 274-280
+
Select (22 or 232 or 238 or 272) and (sidechain or alpha)
-
Color [255,255,0]
+
Wireframe 300
-
Select 225-229
+
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]
Color [255,128,0]
-
select (275 or 276 or 280) and (sidechain or alpha)
+
Select (233 or 234) and (sidechain or alpha)
-
wireframe 250
+
Wireframe 300
-
select (275 or 276 or 280) and (sidechain)
+
Select (233 or 234) and sidechain
-
color cpk
+
Color CPK
-
select (275 or 276 or 280) and (alpha)
+
Select 187 and (sidechain or alpha)
-
color [128,128,255]
+
Wireframe 300
-
select (274 or 227) and (sidechain or alpha)
+
Select 187 and sidechain
-
wireframe 250
+
Color CPK
-
select (274 or 227) and (sidechain)
+
Select 2
-
color cpk
+
Color [0,0,128]
 +
 
 +
Select 278
 +
 
 +
Color [128,0,0]
{{Clear}}
{{Clear}}
-
==PDB ID: 1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone==
+
==PDB ID: [[1mi3]], Xylose reductase with NAD+==
 +
<scene name='2010_Pingry_SMART_Team_Models/1mi3_final/7'>Xylose reductase with NAD+</scene>
-
<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'/>
 
 +
'''Design description'''
-
select all
+
(β/α)8 secondary structure features colored blue and red.
-
backbone off
+
Three residues involved in NAD+ binding have backbones colored green: E227, N276, R280.
-
spacefill off
+
Two additional residues involved in NADP+ binding but not NAD+ binding have sidechains displayed but backbone uncolored: K274 or S275.
-
cartoon off
+
Other residues involved in cofactor binding: S233, V234, W187, Y217
-
wireframe off
+
Loops that make a conformational change to bind NAD+ or NADP+ colored yellow.
-
backbone 300
+
Amino terminus colored dark blue: [0,0,128].
-
color white
+
Carboxyl terminus colored cherry: [128,0,0].
-
select hetero and not water
+
NAD+ shown in wireframe.
-
wireframe 250
 
-
color cpk
+
'''Design script'''
 +
Select all
 +
Cartoon off
-
select sheet
+
Spacefill off
-
color [255, 128, 128]
+
Backbone 350
 +
Color white
 +
Select nad
-
select 274-284 or 253-263 or 200-209 or 170-177 or 145-156 or 92-106 or 58-70 or 31-43
+
Wireframe 250
-
color [128, 255, 255]
+
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 (54 or 86 or 118 or 120 or 122 or 128 or 129 or 137 or 139 or 227) and (sidechain)
+
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
wireframe 250
 +
 +
select 217 and sidechain
color cpk
color cpk
-
select (50 or 55 or 84) and (sidechain)
+
Select 4
-
wireframe 250
+
Color [0,0,128]
-
color [128,0,128]
+
Select 322
-
select (28 or 224) and (sidechain)
+
Color [128,0,0]
-
wireframe 250
+
{{Clear}}
-
color [0,255,0]
+
==PDB ID: [[1afs]], Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone==
 +
<scene name='2010_Pingry_SMART_Team_Models/1afs_final2/1'>Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone</scene>
 +
'''Model description'''
-
select (24 or 166 or 167 or 190 or 216 or 219 or 221 or 270 or 271 or 272 or 276) and (sidechain)
 
-
wireframe 250
+
'''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 [255,127,0]
+
color [0,0,255]
-
select 116-142 and backbone
+
select 217-235 and backbone
-
color [0,0,255]
+
color [0,0,255]
-
select 217-235 and backbone
+
Select 1
-
color [0,0,255]
+
Color [0,0,128]
 +
Select 319
-
+
Color [128,0,0]
{{Clear}}
{{Clear}}

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