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2Y3I
Asym. Unit
Info
Asym.Unit (202 KB)
Biol.Unit 1 (132 KB)
Biol.Unit 2 (66 KB)
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(1)
Title
:
THE STRUCTURE OF THE FULLY CLOSED CONFORMATION OF HUMAN PGK IN COMPLEX WITH L-ADP, 3PG AND THE TSA ALUMINIUM TETRAFLUORIDE
Authors
:
M. W. Bowler, L. Chaloin, C. Lionne
Date
:
21 Dec 10 (Deposition) - 27 Apr 11 (Release) - 29 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,D
Biol. Unit 1: A (1x)
Biol. Unit 2: D (1x)
Keywords
:
Transferase, Aids, Hepatitis, Cancer, L-Nucleoside Analogues, Glycolysis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Lallemand, L. Chaloin, B. Roy, T. Barman, M. W. Bowler, C. Lionne
Interaction Of Human 3-Phosphoglycerate Kinase With Its Two Substrates: Is Substrate Antagonism A Kinetic Advantage?
J. Mol. Biol. V. 409 742 2011
[
close entry info
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Hetero Components
(5, 10)
Info
All Hetero Components
1a: 3-PHOSPHOGLYCERIC ACID (3PGa)
1b: 3-PHOSPHOGLYCERIC ACID (3PGb)
2a: TETRAFLUOROALUMINATE ION (ALFa)
2b: TETRAFLUOROALUMINATE ION (ALFb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
4a: L-ADENOSINE-5'-DIPHOSPHATE (LA8a)
4b: L-ADENOSINE-5'-DIPHOSPHATE (LA8b)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3PG
2
Ligand/Ion
3-PHOSPHOGLYCERIC ACID
2
ALF
2
Ligand/Ion
TETRAFLUOROALUMINATE ION
3
CL
2
Ligand/Ion
CHLORIDE ION
4
LA8
2
Ligand/Ion
L-ADENOSINE-5'-DIPHOSPHATE
5
MG
2
Ligand/Ion
MAGNESIUM ION
[
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:374 , LA8 A:1418 , ALF A:1419
BINDING SITE FOR RESIDUE MG A1416
02
AC2
SOFTWARE
GLY D:213 , ALA D:214 , LYS D:215 , LYS D:219 , ASN D:336 , PRO D:338 , GLY D:340 , GLU D:343 , GLY D:372 , GLY D:373 , ASP D:374 , THR D:375 , ALF D:1417 , MG D:1418
BINDING SITE FOR RESIDUE LA8 D1416
03
AC3
SOFTWARE
LYS A:215 , ALA A:217 , ASP A:218
BINDING SITE FOR RESIDUE CL A1417
04
AC4
SOFTWARE
ARG D:38 , LYS D:215 , LYS D:219 , GLY D:372 , GLY D:373 , GLY D:395 , GLY D:396 , LA8 D:1416 , MG D:1418 , 3PG D:1420 , HOH D:2005
BINDING SITE FOR RESIDUE ALF D1417
05
AC5
SOFTWARE
ASP D:374 , LA8 D:1416 , ALF D:1417
BINDING SITE FOR RESIDUE MG D1418
06
AC6
SOFTWARE
ARG D:65 , LYS D:215 , ASP D:218
BINDING SITE FOR RESIDUE CL D1419
07
AC7
SOFTWARE
GLY A:213 , ALA A:214 , LYS A:215 , LYS A:219 , PHE A:291 , ASN A:336 , PRO A:338 , GLY A:340 , VAL A:341 , PHE A:342 , GLU A:343 , GLY A:372 , GLY A:373 , ASP A:374 , THR A:375 , MG A:1416 , ALF A:1419 , HOH A:2008
BINDING SITE FOR RESIDUE LA8 A1418
08
AC8
SOFTWARE
ARG A:38 , LYS A:215 , LYS A:219 , GLY A:372 , GLY A:373 , ASP A:374 , GLY A:395 , GLY A:396 , MG A:1416 , LA8 A:1418 , 3PG A:1420
BINDING SITE FOR RESIDUE ALF A1419
09
AC9
SOFTWARE
ASP D:23 , ASN D:25 , ARG D:38 , HIS D:62 , ARG D:65 , ARG D:122 , GLY D:166 , ARG D:170 , LYS D:215 , ALF D:1417 , HOH D:2005
BINDING SITE FOR RESIDUE 3PG D1420
10
BC1
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 , LYS A:215 , ALF A:1419
BINDING SITE FOR RESIDUE 3PG A1420
[
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SAPs(SNPs)/Variants
(11, 22)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_006076 (L87P, chain A/D, )
02: VAR_006077 (G157V, chain A/D, )
03: VAR_006078 (D163V, chain A/D, )
04: VAR_006080 (R205P, chain A/D, )
05: VAR_006081 (E251A, chain A/D, )
06: VAR_006082 (V265M, chain A/D, )
07: VAR_006083 (D267N, chain A/D, )
08: VAR_006084 (D284V, chain A/D, )
09: VAR_006085 (D314N, chain A/D, )
10: VAR_006086 (C315R, chain A/D, )
11: VAR_006087 (T351N, chain A/D, )
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/D
L
87
P
02
UniProt
VAR_006077
G
158
V
PGK1_HUMAN
Disease (PGK1D)
---
A/D
G
157
V
03
UniProt
VAR_006078
D
164
V
PGK1_HUMAN
Disease (PGK1D)
---
A/D
D
163
V
04
UniProt
VAR_006080
R
206
P
PGK1_HUMAN
Disease (PGK1D)
---
A/D
R
205
P
05
UniProt
VAR_006081
E
252
A
PGK1_HUMAN
Disease (PGK1D)
---
A/D
E
251
A
06
UniProt
VAR_006082
V
266
M
PGK1_HUMAN
Disease (PGK1D)
---
A/D
V
265
M
07
UniProt
VAR_006083
D
268
N
PGK1_HUMAN
Unclassified
---
A/D
D
267
N
08
UniProt
VAR_006084
D
285
V
PGK1_HUMAN
Disease (PGK1D)
---
A/D
D
284
V
09
UniProt
VAR_006085
D
315
N
PGK1_HUMAN
Disease (PGK1D)
---
A/D
D
314
N
10
UniProt
VAR_006086
C
316
R
PGK1_HUMAN
Disease (PGK1D)
---
A/D
C
315
R
11
UniProt
VAR_006087
T
352
N
PGK1_HUMAN
Polymorphism
---
A/D
T
351
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PGLYCERATE_KINASE (A:17-27,D: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
D:17-27
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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_d2y3ia_ (A:)
1b: SCOP_d2y3id_ (D:)
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Classes
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)
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)
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)
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)
(
)
Families
(
)
(
)
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
d2y3ia_
A:
1b
d2y3id_
D:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PGK_2y3iD01 (D:7-405)
1b: PFAM_PGK_2y3iD02 (D:7-405)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: PGK]
(23)
Family
:
PGK
(23)
Homo sapiens (Human)
(12)
1a
PGK-2y3iD01
D:7-405
1b
PGK-2y3iD02
D:7-405
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Asymmetric Unit 1
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Asym.Unit (202 KB)
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