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2BH9
Asym. Unit
Info
Asym.Unit (92 KB)
Biol.Unit 1 (171 KB)
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(1)
Title
:
X-RAY STRUCTURE OF A DELETION VARIANT OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE COMPLEXED WITH STRUCTURAL AND COENZYME NADP
Authors
:
S. Gover, L. Vandeputte-Rutten, S. W. N. Au, M. J. Adams
Date
:
08 Jan 05 (Deposition) - 25 Apr 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Oxidoreductase, Oxidoreductase (Choh(D)-Nadp), Carbohydrate Metabolism, Glucose Metabolism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kotaka, S. Gover, L. Vandeputte-Rutten, S. W. N. Au, V. M. S. Lam, M. J. Adams
Structural Studies Of Glucose-6-Phosphate And Nadp+ Binding To Human Glucose-6-Phosphate Dehydrogenase
Acta Crystallogr. , Sect. D V. 61 495 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:38 , SER A:40 , GLY A:41 , ASP A:42 , LEU A:43 , ARG A:72 , SER A:73 , GLN A:111 , TYR A:112 , ASP A:114 , ALA A:141 , LEU A:142 , PRO A:143 , TYR A:147 , GLU A:170 , LYS A:171 , HOH A:2154 , HOH A:2155
BINDING SITE FOR RESIDUE NAP A 799
2
AC2
SOFTWARE
LYS A:238 , LYS A:366 , ARG A:370 , ARG A:393 , TYR A:401 , LYS A:403 , ASP A:421 , THR A:423 , ARG A:487 , ASP A:493 , PHE A:501 , TYR A:503 , TYR A:507 , TRP A:509 , HOH A:2152 , HOH A:2157 , HOH A:2159 , HOH A:2161
BINDING SITE FOR RESIDUE NAP A 811
3
AC3
SOFTWARE
GLY A:248 , TYR A:249 , GLU A:252 , THR A:327
BINDING SITE FOR RESIDUE GOL A1516
4
AC4
SOFTWARE
PRO A:467 , GLN A:471 , LEU A:474 , HOH A:2162
BINDING SITE FOR RESIDUE GOL A1517
[
close Site info
]
SAPs(SNPs)/Variants
(64, 64)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_002451 (H32R, chain A, )
02: VAR_002453 (A44G, chain A, )
03: VAR_002454 (I48T, chain A, )
04: VAR_002455 (D58N, chain A, )
05: VAR_002456 (V68M, chain A, )
06: VAR_002457 (Y70H, chain A, )
07: VAR_002458 (L75P, chain A, )
08: VAR_002460 (R81C, chain A, )
09: VAR_002459 (R81H, chain A, )
10: VAR_002461 (S106C, chain A, )
11: VAR_002462 (N126D, chain A, )
12: VAR_002463 (L128P, chain A, )
13: VAR_002464 (G131V, chain A, )
14: VAR_002465 (E156K, chain A, )
15: VAR_002467 (G163D, chain A, )
16: VAR_002466 (G163S, chain A, )
17: VAR_002468 (N165D, chain A, )
18: VAR_002469 (R166H, chain A, )
19: VAR_002470 (D176G, chain A, )
20: VAR_002471 (D181V, chain A, )
21: VAR_002472 (R182W, chain A, )
22: VAR_002473 (S188F, chain A, )
23: VAR_002474 (R198C, chain A, )
24: VAR_002475 (R198P, chain A, )
25: VAR_002476 (M212V, chain A, )
26: VAR_002477 (V213L, chain A, )
27: VAR_002478 (F216L, chain A, )
28: VAR_002480 (R227L, chain A, )
29: VAR_002479 (R227Q, chain A, )
30: VAR_002482 (R257G, chain A, )
31: VAR_002483 (E274K, chain A, )
32: VAR_002484 (S278F, chain A, )
33: VAR_002485 (T279S, chain A, )
34: VAR_002486 (D282H, chain A, )
35: VAR_002487 (R285H, chain A, )
36: VAR_002488 (V291M, chain A, )
37: VAR_002489 (E317K, chain A, )
38: VAR_020535 (Y322H, chain A, )
39: VAR_002490 (L323P, chain A, )
40: VAR_002491 (A335T, chain A, )
41: VAR_002492 (L342F, chain A, )
42: VAR_002493 (P353S, chain A, )
43: VAR_002494 (N363K, chain A, )
44: VAR_002495 (C385R, chain A, )
45: VAR_002496 (K386E, chain A, )
46: VAR_002498 (R387C, chain A, )
47: VAR_002497 (R387H, chain A, )
48: VAR_002499 (R393H, chain A, )
49: VAR_002500 (V394L, chain A, )
50: VAR_002501 (P396L, chain A, )
51: VAR_002502 (E398K, chain A, )
52: VAR_002503 (G410C, chain A, )
53: VAR_002504 (G410D, chain A, )
54: VAR_002505 (E416K, chain A, )
55: VAR_002506 (R439P, chain A, )
56: VAR_002507 (L440F, chain A, )
57: VAR_002508 (G447R, chain A, )
58: VAR_002509 (Q449H, chain A, )
59: VAR_002510 (R454C, chain A, )
60: VAR_002511 (R454H, chain A, )
61: VAR_002512 (R459L, chain A, )
62: VAR_002513 (R459P, chain A, )
63: VAR_002514 (R463H, chain A, )
64: VAR_002515 (G488V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_002451
H
32
R
G6PD_HUMAN
Disease (NSHA)
---
A
H
32
R
02
UniProt
VAR_002453
A
44
G
G6PD_HUMAN
Disease (NSHA)
---
A
A
44
G
03
UniProt
VAR_002454
I
48
T
G6PD_HUMAN
Disease (NSHA)
---
A
I
48
T
04
UniProt
VAR_002455
D
58
N
G6PD_HUMAN
Disease (NSHA)
---
A
D
58
N
05
UniProt
VAR_002456
V
68
M
G6PD_HUMAN
Disease (NSHA)
1050828
A
V
68
M
06
UniProt
VAR_002457
Y
70
H
G6PD_HUMAN
Disease (NSHA)
---
A
Y
70
H
07
UniProt
VAR_002458
L
75
P
G6PD_HUMAN
Disease (NSHA)
---
A
L
75
P
08
UniProt
VAR_002460
R
81
C
G6PD_HUMAN
Disease (NSHA)
138687036
A
R
81
C
09
UniProt
VAR_002459
R
81
H
G6PD_HUMAN
Disease (NSHA)
---
A
R
81
H
10
UniProt
VAR_002461
S
106
C
G6PD_HUMAN
Disease (NSHA)
---
A
S
106
C
11
UniProt
VAR_002462
N
126
D
G6PD_HUMAN
Disease (NSHA)
1050829
A
N
126
D
12
UniProt
VAR_002463
L
128
P
G6PD_HUMAN
Disease (NSHA)
---
A
L
128
P
13
UniProt
VAR_002464
G
131
V
G6PD_HUMAN
Polymorphism
137852341
A
G
131
V
14
UniProt
VAR_002465
E
156
K
G6PD_HUMAN
Disease (NSHA)
---
A
E
156
K
15
UniProt
VAR_002467
G
163
D
G6PD_HUMAN
Disease (NSHA)
---
A
G
163
D
16
UniProt
VAR_002466
G
163
S
G6PD_HUMAN
Disease (NSHA)
---
A
G
163
S
17
UniProt
VAR_002468
N
165
D
G6PD_HUMAN
Disease (NSHA)
---
A
N
165
D
18
UniProt
VAR_002469
R
166
H
G6PD_HUMAN
Disease (NSHA)
---
A
R
166
H
19
UniProt
VAR_002470
D
176
G
G6PD_HUMAN
Disease (NSHA)
---
A
D
176
G
20
UniProt
VAR_002471
D
181
V
G6PD_HUMAN
Disease (NSHA)
5030872
A
D
181
V
21
UniProt
VAR_002472
R
182
W
G6PD_HUMAN
Disease (NSHA)
---
A
R
182
W
22
UniProt
VAR_002473
S
188
F
G6PD_HUMAN
Disease (NSHA)
5030868
A
S
188
F
23
UniProt
VAR_002474
R
198
C
G6PD_HUMAN
Disease (NSHA)
---
A
R
198
C
24
UniProt
VAR_002475
R
198
P
G6PD_HUMAN
Disease (NSHA)
---
A
R
198
P
25
UniProt
VAR_002476
M
212
V
G6PD_HUMAN
Disease (NSHA)
---
A
M
212
V
26
UniProt
VAR_002477
V
213
L
G6PD_HUMAN
Disease (NSHA)
---
A
V
213
L
27
UniProt
VAR_002478
F
216
L
G6PD_HUMAN
Disease (NSHA)
---
A
F
216
L
28
UniProt
VAR_002480
R
227
L
G6PD_HUMAN
Disease (NSHA)
---
A
R
227
L
29
UniProt
VAR_002479
R
227
Q
G6PD_HUMAN
Disease (NSHA)
---
A
R
227
Q
30
UniProt
VAR_002482
R
257
G
G6PD_HUMAN
Disease (NSHA)
---
A
R
257
G
31
UniProt
VAR_002483
E
274
K
G6PD_HUMAN
Disease (NSHA)
---
A
E
274
K
32
UniProt
VAR_002484
S
278
F
G6PD_HUMAN
Disease (NSHA)
---
A
S
278
F
33
UniProt
VAR_002485
T
279
S
G6PD_HUMAN
Disease (NSHA)
---
A
T
279
S
34
UniProt
VAR_002486
D
282
H
G6PD_HUMAN
Disease (NSHA)
---
A
D
282
H
35
UniProt
VAR_002487
R
285
H
G6PD_HUMAN
Disease (NSHA)
---
A
R
285
H
36
UniProt
VAR_002488
V
291
M
G6PD_HUMAN
Disease (NSHA)
---
A
V
291
M
37
UniProt
VAR_002489
E
317
K
G6PD_HUMAN
Disease (NSHA)
---
A
E
317
K
38
UniProt
VAR_020535
Y
322
H
G6PD_HUMAN
Unclassified
---
A
Y
322
H
39
UniProt
VAR_002490
L
323
P
G6PD_HUMAN
Disease (NSHA)
76723693
A
L
323
P
40
UniProt
VAR_002491
A
335
T
G6PD_HUMAN
Disease (NSHA)
5030869
A
A
335
T
41
UniProt
VAR_002492
L
342
F
G6PD_HUMAN
Unclassified
---
A
L
342
F
42
UniProt
VAR_002493
P
353
S
G6PD_HUMAN
Disease (NSHA)
---
A
P
353
S
43
UniProt
VAR_002494
N
363
K
G6PD_HUMAN
Disease (NSHA)
---
A
N
363
K
44
UniProt
VAR_002495
C
385
R
G6PD_HUMAN
Disease (NSHA)
---
A
C
385
R
45
UniProt
VAR_002496
K
386
E
G6PD_HUMAN
Disease (NSHA)
---
A
K
386
E
46
UniProt
VAR_002498
R
387
C
G6PD_HUMAN
Disease (NSHA)
---
A
R
387
C
47
UniProt
VAR_002497
R
387
H
G6PD_HUMAN
Disease (NSHA)
---
A
R
387
H
48
UniProt
VAR_002499
R
393
H
G6PD_HUMAN
Disease (NSHA)
---
A
R
393
H
49
UniProt
VAR_002500
V
394
L
G6PD_HUMAN
Disease (NSHA)
---
A
V
394
L
50
UniProt
VAR_002501
P
396
L
G6PD_HUMAN
Disease (NSHA)
---
A
P
396
L
51
UniProt
VAR_002502
E
398
K
G6PD_HUMAN
Disease (NSHA)
---
A
E
398
K
52
UniProt
VAR_002503
G
410
C
G6PD_HUMAN
Disease (NSHA)
---
A
G
410
C
53
UniProt
VAR_002504
G
410
D
G6PD_HUMAN
Disease (NSHA)
---
A
G
410
D
54
UniProt
VAR_002505
E
416
K
G6PD_HUMAN
Disease (NSHA)
---
A
E
416
K
55
UniProt
VAR_002506
R
439
P
G6PD_HUMAN
Disease (NSHA)
---
A
R
439
P
56
UniProt
VAR_002507
L
440
F
G6PD_HUMAN
Disease (NSHA)
---
A
L
440
F
57
UniProt
VAR_002508
G
447
R
G6PD_HUMAN
Disease (NSHA)
---
A
G
447
R
58
UniProt
VAR_002509
Q
449
H
G6PD_HUMAN
Disease (NSHA)
---
A
Q
449
H
59
UniProt
VAR_002510
R
454
C
G6PD_HUMAN
Disease (NSHA)
---
A
R
454
C
60
UniProt
VAR_002511
R
454
H
G6PD_HUMAN
Unclassified
---
A
R
454
H
61
UniProt
VAR_002512
R
459
L
G6PD_HUMAN
Disease (NSHA)
72554665
A
R
459
L
62
UniProt
VAR_002513
R
459
P
G6PD_HUMAN
Disease (NSHA)
72554665
A
R
459
P
63
UniProt
VAR_002514
R
463
H
G6PD_HUMAN
Disease (NSHA)
---
A
R
463
H
64
UniProt
VAR_002515
G
488
V
G6PD_HUMAN
Disease (NSHA)
---
A
G
488
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: G6P_DEHYDROGENASE (A:200-206)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
G6P_DEHYDROGENASE
PS00069
Glucose-6-phosphate dehydrogenase active site.
G6PD_HUMAN
200-206
1
A:200-206
[
close PROSITE info
]
Exons
(12, 12)
Info
All Exons
Exon 1.3a (A:27-40)
Exon 1.4 (A:41-53)
Exon 1.5a (A:53-89)
Exon 1.6a (A:90-162)
Exon 1.7b (A:162-215)
Exon 1.8c (A:215-257)
Exon 1.9b (A:257-288)
Exon 1.10c (A:289-351)
Exon 1.10e (A:351-429)
Exon 1.11 (A:430-455)
Exon 1.12b (A:455-486)
Exon 1.12d (A:486-515)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.3a
02: Boundary 1.3a/1.4
03: Boundary 1.4/1.5a
04: Boundary 1.5a/1.6a
05: Boundary 1.6a/1.7b
06: Boundary 1.7b/1.8c
07: Boundary 1.8c/1.9b
08: Boundary 1.9b/1.10c
09: Boundary 1.10c/1.10e
10: Boundary 1.10e/1.11
11: Boundary 1.11/1.12b
12: Boundary 1.12b/1.12d
13: Boundary 1.12d/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000393564
1a
ENSE00001450454
X:153775787-153775683
105
G6PD_HUMAN
-
0
0
-
-
1.3a
ENST00000393564
3a
ENSE00001629012
X:153774378-153774251
128
G6PD_HUMAN
1-40
40
1
A:27-40
14
1.4
ENST00000393564
4
ENSE00001050596
X:153764393-153764356
38
G6PD_HUMAN
41-53
13
1
A:41-53
13
1.5a
ENST00000393564
5a
ENSE00001200322
X:153764260-153764152
109
G6PD_HUMAN
53-89
37
1
A:53-89
37
1.6a
ENST00000393564
6a
ENSE00001050603
X:153763600-153763383
218
G6PD_HUMAN
90-162
73
1
A:90-162
73
1.7b
ENST00000393564
7b
ENSE00001050595
X:153762711-153762553
159
G6PD_HUMAN
162-215
54
1
A:162-215
54
1.8c
ENST00000393564
8c
ENSE00001050598
X:153762375-153762250
126
G6PD_HUMAN
215-257
43
1
A:215-257
43
1.9b
ENST00000393564
9b
ENSE00001050601
X:153761884-153761791
94
G6PD_HUMAN
257-288
32
1
A:257-288
32
1.10c
ENST00000393564
10c
ENSE00001050608
X:153761343-153761157
187
G6PD_HUMAN
289-351
63
1
A:289-351
63
1.10e
ENST00000393564
10e
ENSE00001050602
X:153761017-153760782
236
G6PD_HUMAN
351-429
79
1
A:351-429
79
1.11
ENST00000393564
11
ENSE00001050597
X:153760677-153760601
77
G6PD_HUMAN
430-455
26
1
A:430-455
26
1.12b
ENST00000393564
12b
ENSE00001050600
X:153760495-153760403
93
G6PD_HUMAN
455-486
32
1
A:455-486
32
1.12d
ENST00000393564
12d
ENSE00001515849
X:153760305-153760215
91
G6PD_HUMAN
486-515
30
1
A:486-515
30
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2bh9A02 (A:200-432,A:454-515)
2a: CATH_2bh9A01 (A:27-199,A:433-453)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Human (Homo sapiens)
(8)
1a
2bh9A02
A:200-432,A:454-515
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
2bh9A01
A:27-199,A:433-453
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
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by Rainbow (Group)
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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close Script example commands
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
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Asym.Unit (92 KB)
Header - Asym.Unit
Biol.Unit 1 (171 KB)
Header - Biol.Unit 1
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