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13PK
Biol. Unit 1
Info
Asym.Unit (276 KB)
Biol.Unit 1 (72 KB)
Biol.Unit 2 (71 KB)
Biol.Unit 3 (71 KB)
Biol.Unit 4 (71 KB)
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(1)
Title
:
TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI
Authors
:
B. E. Bernstein, P. A. M. Michels, W. G. J. Hol
Date
:
23 Nov 96 (Deposition) - 24 Dec 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Kinase, Phosphoglycerate, Ternary Complex, Glycolysis, Transferase
(Keyword Search:
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Reference
:
B. E. Bernstein, P. A. Michels, W. G. Hol
Synergistic Effects Of Substrate-Induced Conformational Changes In Phosphoglycerate Kinase Activation.
Nature V. 385 275 1997
(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)
2b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
2d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
4d: PHOSPHATE ION (PO4d)
4e: PHOSPHATE ION (PO4e)
4f: PHOSPHATE ION (PO4f)
View:
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Label:
No.
Name
Count
Type
Full Name
1
3PG
1
Ligand/Ion
3-PHOSPHOGLYCERIC ACID
2
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
PO4
2
Ligand/Ion
PHOSPHATE ION
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC7 (SOFTWARE)
3: BC1 (SOFTWARE)
4: BC2 (SOFTWARE)
5: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:377 , ADP A:421
BINDING SITE FOR RESIDUE MG A 422
2
AC7
SOFTWARE
LEU A:103 , ARG A:105 , PHE D:344 , GLU D:345 , LEU D:384
BINDING SITE FOR RESIDUE PO4 A 701
3
BC1
SOFTWARE
PHE A:344 , VAL A:347 , LEU A:384 , HOH A:789 , LYS D:48 , LEU D:103
BINDING SITE FOR RESIDUE PO4 A 704
4
BC2
SOFTWARE
GLY A:217 , ALA A:218 , LYS A:219 , LYS A:223 , GLY A:241 , TYR A:245 , ALA A:314 , LEU A:315 , ASN A:338 , PRO A:340 , GLY A:342 , VAL A:343 , GLU A:345 , GLY A:374 , GLY A:375 , GLY A:376 , ASP A:377 , SER A:378 , MG A:422 , HOH A:716 , HOH A:722 , HOH A:842 , HOH A:861
BINDING SITE FOR RESIDUE ADP A 421
5
BC3
SOFTWARE
ASP A:24 , ASN A:26 , ARG A:39 , HIS A:62 , ARG A:65 , ARG A:135 , GLY A:168 , ARG A:172 , LYS A:219 , HOH A:724 , HOH A:752 , HOH A:842 , HOH A:876
BINDING SITE FOR RESIDUE 3PG A 423
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_PGKC_TRYBB_001 (G75D, chain A, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_PGKC_TRYBB_001
*
G
75
D
PGKC_TRYBB
---
---
A
G
75
D
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PGLYCERATE_KINASE (A:18-28)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PGLYCERATE_KINASE
PS00111
Phosphoglycerate kinase signature.
PGKC_TRYBB
18-28
1
A:18-28
-
-
-
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d13pka_ (A:)
1b: SCOP_d13pkb_ (B:)
1c: SCOP_d13pkc_ (C:)
1d: SCOP_d13pkd_ (D:)
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Protein Domains
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Organisms
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(
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphoglycerate kinase
(42)
Superfamily
:
Phosphoglycerate kinase
(42)
Family
:
Phosphoglycerate kinase
(39)
Protein domain
:
Phosphoglycerate kinase
(16)
Trypanosome (Trypanosoma brucei) [TaxId: 5691]
(2)
1a
d13pka_
A:
1b
d13pkb_
B:
1c
d13pkc_
C:
1d
d13pkd_
D:
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_13pkA01 (A:5-192)
1b: CATH_13pkB01 (B:5-192)
1c: CATH_13pkC01 (C:5-192)
1d: CATH_13pkD01 (D:5-192)
2a: CATH_13pkA02 (A:199-406)
2b: CATH_13pkB02 (B:199-406)
2c: CATH_13pkC02 (C:199-406)
2d: CATH_13pkD02 (D:199-406)
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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)
Trypanosoma brucei. Organism_taxid: 5691. Variant: glycosomal version.
(2)
1a
13pkA01
A:5-192
1b
13pkB01
B:5-192
1c
13pkC01
C:5-192
1d
13pkD01
D:5-192
Homologous Superfamily
:
[code=3.40.50.1270, no name defined]
(25)
Trypanosoma brucei. Organism_taxid: 5691. Variant: glycosomal version.
(2)
2a
13pkA02
A:199-406
2b
13pkB02
B:199-406
2c
13pkC02
C:199-406
2d
13pkD02
D:199-406
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Pfam Domains
(0, 0)
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Chain A
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (276 KB)
Header - Asym.Unit
Biol.Unit 1 (72 KB)
Header - Biol.Unit 1
Biol.Unit 2 (71 KB)
Header - Biol.Unit 2
Biol.Unit 3 (71 KB)
Header - Biol.Unit 3
Biol.Unit 4 (71 KB)
Header - Biol.Unit 4
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