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2ZYA
Asym. Unit
Info
Asym.Unit (180 KB)
Biol.Unit 1 (174 KB)
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(1)
Title
:
DIMERIC 6-PHOSPHOGLUCONATE DEHYDROGENASE COMPLEXED WITH 6-PHOSPHOGLUCONATE
Authors
:
Y. -Y. Chen, T. -P. Ko, L. -P. Lo, C. -H. Lin, A. H. -J. Wang
Date
:
19 Jan 09 (Deposition) - 01 Sep 09 (Release) - 22 Jan 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Nadp, Pentose Phosphate Pathway, Oxidoreductase, 6-Phosphogluconate Dehydrogenase, 6-Phosphogluconate, Gluconate Utilization, Pentose Shunt
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. -Y. Chen, T. -P. Ko, W. -H. Chen, L. -P. Lo, C. -H. Lin, A. H. -J. Wang
Conformational Changes Associated With Cofactor/Substrate Binding Of 6-Phosphogluconate Dehydrogenase From Escherichi Coli And Klebsiella Pneumoniae: Implications For Enzyme Mechanism
J. Struct. Biol. V. 169 25 2010
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: 6-PHOSPHOGLUCONIC ACID (6PGa)
1b: 6-PHOSPHOGLUCONIC ACID (6PGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6PG
2
Ligand/Ion
6-PHOSPHOGLUCONIC ACID
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:102 , SER A:128 , GLY A:129 , GLY A:130 , LYS A:183 , HIS A:186 , ASN A:187 , GLU A:190 , TYR A:191 , ASN A:259 , LYS A:260 , ARG A:287 , ILE A:365 , HOH A:656 , HOH A:657 , HOH A:714 , HOH A:946 , ARG B:445 , PHE B:448 , HIS B:451
BINDING SITE FOR RESIDUE 6PG A2002
2
AC2
SOFTWARE
ARG A:445 , PHE A:448 , HIS A:451 , ASN B:102 , SER B:128 , GLY B:129 , GLY B:130 , LYS B:183 , HIS B:186 , ASN B:187 , GLU B:190 , TYR B:191 , LYS B:260 , ARG B:287 , ILE B:365 , HOH B:661 , HOH B:839 , HOH B:915 , HOH B:928 , HOH B:1264
BINDING SITE FOR RESIDUE 6PG B2001
[
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SAPs(SNPs)/Variants
(21, 42)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_6PGD_ECOLI_001 (S2L, chain A/B, )
02: VAR_6PGD_ECOLI_002 (F32Y, chain A/B, )
03: VAR_6PGD_ECOLI_003 (T39Q, chain A/B, )
04: VAR_6PGD_ECOLI_004 (V52D, chain A/B, )
05: VAR_6PGD_ECOLI_005 (Y55F, chain A/B, )
06: VAR_6PGD_ECOLI_006 (N102K, chain A/B, )
07: VAR_6PGD_ECOLI_007 (A117S, chain A/B, )
08: VAR_6PGD_ECOLI_008 (V170F, chain A/B, )
09: VAR_6PGD_ECOLI_009 (A175S, chain A/B, )
10: VAR_6PGD_ECOLI_010 (N209S, chain A/B, )
11: VAR_6PGD_ECOLI_011 (T211S, chain A/B, )
12: VAR_6PGD_ECOLI_012 (A216T, chain A/B, )
13: VAR_6PGD_ECOLI_013 (D294E, chain A/B, )
14: VAR_6PGD_ECOLI_014 (A308G, chain A/B, )
15: VAR_6PGD_ECOLI_015 (D313N, chain A/B, )
16: VAR_6PGD_ECOLI_016 (A315G, chain A/B, )
17: VAR_6PGD_ECOLI_017 (L325Q, chain A/B, )
18: VAR_6PGD_ECOLI_018 (I330S, chain A/B, )
19: VAR_6PGD_ECOLI_019 (D350A, chain A/B, )
20: VAR_6PGD_ECOLI_020 (Q369R, chain A/B, )
21: VAR_6PGD_ECOLI_021 (S422A, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_6PGD_ECOLI_001
*
S
2
L
6PGD_ECOLI
---
---
A/B
S
2
L
02
UniProt
VAR_6PGD_ECOLI_002
*
F
32
Y
6PGD_ECOLI
---
---
A/B
F
32
Y
03
UniProt
VAR_6PGD_ECOLI_003
*
T
39
Q
6PGD_ECOLI
---
---
A/B
T
39
Q
04
UniProt
VAR_6PGD_ECOLI_004
*
V
52
D
6PGD_ECOLI
---
---
A/B
V
52
D
05
UniProt
VAR_6PGD_ECOLI_005
*
Y
55
F
6PGD_ECOLI
---
---
A/B
Y
55
F
06
UniProt
VAR_6PGD_ECOLI_006
*
N
102
K
6PGD_ECOLI
---
---
A/B
N
102
K
07
UniProt
VAR_6PGD_ECOLI_007
*
A
117
S
6PGD_ECOLI
---
---
A/B
A
117
S
08
UniProt
VAR_6PGD_ECOLI_008
*
V
170
F
6PGD_ECOLI
---
---
A/B
V
170
F
09
UniProt
VAR_6PGD_ECOLI_009
*
A
175
S
6PGD_ECOLI
---
---
A/B
A
175
S
10
UniProt
VAR_6PGD_ECOLI_010
*
N
209
S
6PGD_ECOLI
---
---
A/B
N
209
S
11
UniProt
VAR_6PGD_ECOLI_011
*
T
211
S
6PGD_ECOLI
---
---
A/B
T
211
S
12
UniProt
VAR_6PGD_ECOLI_012
*
A
216
T
6PGD_ECOLI
---
---
A/B
A
216
T
13
UniProt
VAR_6PGD_ECOLI_013
*
D
294
E
6PGD_ECOLI
---
---
A/B
D
294
E
14
UniProt
VAR_6PGD_ECOLI_014
*
A
308
G
6PGD_ECOLI
---
---
A/B
A
308
G
15
UniProt
VAR_6PGD_ECOLI_015
*
D
313
N
6PGD_ECOLI
---
---
A/B
D
313
N
16
UniProt
VAR_6PGD_ECOLI_016
*
A
315
G
6PGD_ECOLI
---
---
A/B
A
315
G
17
UniProt
VAR_6PGD_ECOLI_017
*
L
325
Q
6PGD_ECOLI
---
---
A/B
L
325
Q
18
UniProt
VAR_6PGD_ECOLI_018
*
I
330
S
6PGD_ECOLI
---
---
A/B
I
330
S
19
UniProt
VAR_6PGD_ECOLI_019
*
D
350
A
6PGD_ECOLI
---
---
A/B
D
350
A
20
UniProt
VAR_6PGD_ECOLI_020
*
Q
369
R
6PGD_ECOLI
---
---
A/B
Q
369
R
21
UniProt
VAR_6PGD_ECOLI_021
*
S
422
A
6PGD_ECOLI
---
---
A/B
S
422
A
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: 6PGD (A:253-265,B:253-265)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
6PGD
PS00461
6-phosphogluconate dehydrogenase signature.
6PGD_ECOLI
253-265
2
A:253-265
B:253-265
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2zyaa2 (A:177-466)
1b: SCOP_d2zyab2 (B:177-467)
2a: SCOP_d2zyaa1 (A:2-176)
2b: SCOP_d2zyab1 (B:2-176)
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(
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)
Superfamilies
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(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Escherichia coli K-12 [TaxId: 83333]
(3)
1a
d2zyaa2
A:177-466
1b
d2zyab2
B:177-467
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Escherichia coli K-12 [TaxId: 83333]
(7)
2a
d2zyaa1
A:2-176
2b
d2zyab1
B:2-176
[
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]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2zyaA01 (A:2-180)
1b: CATH_2zyaB01 (B:2-180)
2a: CATH_2zyaA02 (A:181-434)
2b: CATH_2zyaB02 (B:181-434)
3a: CATH_2zyaB03 (B:435-467)
3b: CATH_2zyaA03 (A:435-466)
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(
)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli k-12. Organism_taxid: 83333. Strain: k-12.
(3)
1a
2zyaA01
A:2-180
1b
2zyaB01
B:2-180
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(60)
Homologous Superfamily
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(59)
Escherichia coli k-12. Organism_taxid: 83333. Strain: k-12.
(3)
2a
2zyaA02
A:181-434
2b
2zyaB02
B:181-434
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
6-Phosphogluconate Dehydrogenase, domain 3
(20)
Escherichia coli k-12. Organism_taxid: 83333. Strain: k-12.
(3)
3a
2zyaB03
B:435-467
3b
2zyaA03
A:435-466
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_6PGD_2zyaB01 (B:179-467)
1b: PFAM_6PGD_2zyaB02 (B:179-467)
2a: PFAM_NAD_binding_2_2zyaB03 (B:3-175)
2b: PFAM_NAD_binding_2_2zyaB04 (B:3-175)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6PGD_C
(47)
Family
:
6PGD
(10)
Escherichia coli (strain K12)
(2)
1a
6PGD-2zyaB01
B:179-467
1b
6PGD-2zyaB02
B:179-467
Clan
:
NADP_Rossmann
(1239)
Family
:
NAD_binding_2
(15)
Escherichia coli (strain K12)
(2)
2a
NAD_binding_2-2zyaB03
B:3-175
2b
NAD_binding_2-2zyaB04
B:3-175
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