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2WZC
Asym. Unit
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Asym.Unit (78 KB)
Biol.Unit 1 (73 KB)
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(1)
Title
:
THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP, 3PG AND ALUMINIUM TETRAFLUORIDE
Authors
:
M. W. Bowler, M. J. Cliff, J. P. M. Marston, N. J. Baxter, A. M. H. Hownslow A. V. Varga, J. Szabo, M. Vas, G. M. Blackburn, J. P. Waltho
Date
:
27 Nov 09 (Deposition) - 14 Apr 10 (Release) - 07 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hereditary Hemolytic Anemia, Transferase, Phosphoprotein, Kinase, Glycolysis, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Cliff, M. W. Bowler, J. Szabo, J. P. M. Marston, A. V. Varga, A. M. H. Hownslow, N. J. Baxter, G. M. Blackburn, M. Vas, J. P. Waltho
Transition State Analogue Structures Of Human Phosphoglycerate Kinase Establish The Importance Of Charge Balance In Catalysis.
J. Am. Chem. Soc. V. 132 6507 2010
[
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Hetero Components
(5, 5)
Info
All Hetero Components
1a: 3-PHOSPHOGLYCERIC ACID (3PGa)
2a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
3a: TETRAFLUOROALUMINATE ION (ALFa)
4a: CHLORIDE ION (CLa)
5a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3PG
1
Ligand/Ion
3-PHOSPHOGLYCERIC ACID
2
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
3
ALF
1
Ligand/Ion
TETRAFLUOROALUMINATE ION
4
CL
1
Ligand/Ion
CHLORIDE ION
5
MG
1
Ligand/Ion
MAGNESIUM ION
[
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]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:374 , ALF A:1419 , ADP A:1420 , HOH A:2464 , HOH A:2470
BINDING SITE FOR RESIDUE MG A1417
2
AC2
SOFTWARE
ARG A:65 , LYS A:215 , ASP A:218
BINDING SITE FOR RESIDUE CL A1418
3
AC3
SOFTWARE
ARG A:38 , LYS A:215 , LYS A:219 , GLY A:372 , GLY A:373 , GLY A:395 , GLY A:396 , MG A:1417 , ADP A:1420 , 3PG A:1421 , HOH A:2213 , HOH A:2464 , HOH A:2470 , HOH A:2471
BINDING SITE FOR RESIDUE ALF A1419
4
AC4
SOFTWARE
GLY A:213 , ALA A:214 , LYS A:215 , LYS A:219 , GLY A:237 , GLY A:238 , LEU A:256 , GLY A:312 , LEU A:313 , ASN A:336 , PRO A:338 , GLY A:340 , VAL A:341 , GLU A:343 , GLY A:371 , GLY A:372 , GLY A:373 , ASP A:374 , THR A:375 , MG A:1417 , ALF A:1419 , HOH A:2400 , HOH A:2425 , HOH A:2464 , HOH A:2465 , HOH A:2466 , HOH A:2467 , HOH A:2468 , HOH A:2469 , HOH A:2470
BINDING SITE FOR RESIDUE ADP A1420
5
AC5
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 , HOH A:2470 , HOH A:2471 , HOH A:2472 , HOH A:2473
BINDING SITE FOR RESIDUE 3PG A1421
[
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SAPs(SNPs)/Variants
(11, 11)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_006076 (L87P, chain A, )
02: VAR_006077 (G157V, chain A, )
03: VAR_006078 (D163V, chain A, )
04: VAR_006080 (R205P, chain A, )
05: VAR_006081 (E251A, chain A, )
06: VAR_006082 (V265M, chain A, )
07: VAR_006083 (D267N, chain A, )
08: VAR_006084 (D284V, chain A, )
09: VAR_006085 (D314N, chain A, )
10: VAR_006086 (C315R, chain A, )
11: VAR_006087 (T351N, chain A, )
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
L
87
P
02
UniProt
VAR_006077
G
158
V
PGK1_HUMAN
Disease (PGK1D)
---
A
G
157
V
03
UniProt
VAR_006078
D
164
V
PGK1_HUMAN
Disease (PGK1D)
---
A
D
163
V
04
UniProt
VAR_006080
R
206
P
PGK1_HUMAN
Disease (PGK1D)
---
A
R
205
P
05
UniProt
VAR_006081
E
252
A
PGK1_HUMAN
Disease (PGK1D)
---
A
E
251
A
06
UniProt
VAR_006082
V
266
M
PGK1_HUMAN
Disease (PGK1D)
---
A
V
265
M
07
UniProt
VAR_006083
D
268
N
PGK1_HUMAN
Unclassified
---
A
D
267
N
08
UniProt
VAR_006084
D
285
V
PGK1_HUMAN
Disease (PGK1D)
---
A
D
284
V
09
UniProt
VAR_006085
D
315
N
PGK1_HUMAN
Disease (PGK1D)
---
A
D
314
N
10
UniProt
VAR_006086
C
316
R
PGK1_HUMAN
Disease (PGK1D)
---
A
C
315
R
11
UniProt
VAR_006087
T
352
N
PGK1_HUMAN
Polymorphism
---
A
T
351
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PGLYCERATE_KINASE (A: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
1
A: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, 1)
Info
All SCOP Domains
1a: SCOP_d2wzca_ (A:)
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Classes
(
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(
)
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
d2wzca_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2wzcA01 (A:3-188)
2a: CATH_2wzcA02 (A:195-403)
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(
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
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
2wzcA01
A:3-188
Homologous Superfamily
:
[code=3.40.50.1270, no name defined]
(25)
Human (Homo sapiens)
(8)
2a
2wzcA02
A:195-403
[
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_PGK_2wzcA01 (A:7-405)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: PGK]
(23)
Family
:
PGK
(23)
Homo sapiens (Human)
(12)
1a
PGK-2wzcA01
A:7-405
[
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]
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)
Protein
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Solvent
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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