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3C3A
Asym. Unit
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Asym.Unit (135 KB)
Biol.Unit 1 (67 KB)
Biol.Unit 2 (67 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE KINASE BOUND TO 3-PHOSPHOGLYCERATE AND L-ADP
Authors
:
S. T. Arold, C. Gondeau, C. Lionne, L. Chaloin
Date
:
28 Jan 08 (Deposition) - 01 Jul 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protein-Nucleotide Complex, L-Enantiomer Of Adp, Kinase, Acetylation, Atp-Binding, Cytoplasm, Disease Mutation, Glycolysis, Hereditary Hemolytic Anemia, Nucleotide-Binding, Phosphoprotein, Polymorphism, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Gondeau, L. Chaloin, P. Lallemand, B. Roy, C. Perigaud, T. Barman, A. Varga, M. Vas, C. Lionne, S. T. Arold
Molecular Basis For The Lack Of Enantioselectivity Of Human 3-Phosphoglycerate Kinase
Nucleic Acids Res. V. 36 3620 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: 3-PHOSPHOGLYCERIC ACID (3PGa)
1b: 3-PHOSPHOGLYCERIC ACID (3PGb)
2a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
3a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3PG
2
Ligand/Ion
3-PHOSPHOGLYCERIC ACID
2
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
3
MG
1
Ligand/Ion
MAGNESIUM ION
[
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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
ASP B:218
BINDING SITE FOR RESIDUE MG B 417
2
AC2
SOFTWARE
ASP B:23 , ASN B:25 , ARG B:38 , HIS B:62 , ARG B:65 , ARG B:122 , GLY B:166 , THR B:167 , ARG B:170
BINDING SITE FOR RESIDUE 3PG B 418
3
AC3
SOFTWARE
ASP A:23 , ASN A:25 , ARG A:38 , HIS A:62 , ARG A:65 , ARG A:122 , GLY A:166 , ARG A:170
BINDING SITE FOR RESIDUE 3PG A 417
4
AC4
SOFTWARE
GLY B:213 , ALA B:214 , ASP B:218 , LYS B:219 , GLY B:237 , GLY B:238 , GLY B:312 , PRO B:338 , GLY B:340 , GLU B:343
BINDING SITE FOR RESIDUE ADP B 419
[
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]
SAPs(SNPs)/Variants
(11, 22)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_006076 (L87P, chain A/B, )
02: VAR_006077 (G157V, chain A/B, )
03: VAR_006078 (D163V, chain A/B, )
04: VAR_006080 (R205P, chain A/B, )
05: VAR_006081 (E251A, chain A/B, )
06: VAR_006082 (V265M, chain A/B, )
07: VAR_006083 (D267N, chain A/B, )
08: VAR_006084 (D284V, chain A/B, )
09: VAR_006085 (D314N, chain A/B, )
10: VAR_006086 (C315R, chain A/B, )
11: VAR_006087 (T351N, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_006076
L
88
P
PGK1_HUMAN
Disease (PGK1D)
---
A/B
L
87
P
02
UniProt
VAR_006077
G
158
V
PGK1_HUMAN
Disease (PGK1D)
---
A/B
G
157
V
03
UniProt
VAR_006078
D
164
V
PGK1_HUMAN
Disease (PGK1D)
---
A/B
D
163
V
04
UniProt
VAR_006080
R
206
P
PGK1_HUMAN
Disease (PGK1D)
---
A/B
R
205
P
05
UniProt
VAR_006081
E
252
A
PGK1_HUMAN
Disease (PGK1D)
---
A/B
E
251
A
06
UniProt
VAR_006082
V
266
M
PGK1_HUMAN
Disease (PGK1D)
---
A/B
V
265
M
07
UniProt
VAR_006083
D
268
N
PGK1_HUMAN
Unclassified
---
A/B
D
267
N
08
UniProt
VAR_006084
D
285
V
PGK1_HUMAN
Disease (PGK1D)
---
A/B
D
284
V
09
UniProt
VAR_006085
D
315
N
PGK1_HUMAN
Disease (PGK1D)
---
A/B
D
314
N
10
UniProt
VAR_006086
C
316
R
PGK1_HUMAN
Disease (PGK1D)
---
A/B
C
315
R
11
UniProt
VAR_006087
T
352
N
PGK1_HUMAN
Polymorphism
---
A/B
T
351
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PGLYCERATE_KINASE (A:17-27,B:17-27)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PGLYCERATE_KINASE
PS00111
Phosphoglycerate kinase signature.
PGK1_HUMAN
18-28
2
A:17-27
B:17-27
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3c3aa_ (A:)
1b: SCOP_d3c3ab_ (B:)
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphoglycerate kinase
(42)
Superfamily
:
Phosphoglycerate kinase
(42)
Family
:
Phosphoglycerate kinase
(39)
Protein domain
:
automated matches
(23)
Human (Homo sapiens) [TaxId: 9606]
(18)
1a
d3c3aa_
A:
1b
d3c3ab_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3c3aA01 (A:3-188)
1b: CATH_3c3aB01 (B:3-188)
2a: CATH_3c3aA02 (A:195-403)
2b: CATH_3c3aB02 (B:195-403)
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Organisms
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(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1260, no name defined]
(25)
Human (Homo sapiens)
(8)
1a
3c3aA01
A:3-188
1b
3c3aB01
B:3-188
Homologous Superfamily
:
[code=3.40.50.1270, no name defined]
(25)
Human (Homo sapiens)
(8)
2a
3c3aA02
A:195-403
2b
3c3aB02
B:195-403
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (135 KB)
Header - Asym.Unit
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