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13PK
Asym. Unit
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:
[
Gene Ontology, PubMed, Web (Google)
]
)
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
)
[
close entry info
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Hetero Components
(4, 16)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3PG
2
Ligand/Ion
3-PHOSPHOGLYCERIC ACID
2
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
PO4
6
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:377 , ADP A:421
BINDING SITE FOR RESIDUE MG A 422
02
AC2
SOFTWARE
ASP B:377 , ADP B:421
BINDING SITE FOR RESIDUE MG B 422
03
AC3
SOFTWARE
ASP C:377 , ADP C:421 , PO4 C:624
BINDING SITE FOR RESIDUE MG C 422
04
AC4
SOFTWARE
ASP D:377 , ADP D:421 , PO4 D:625
BINDING SITE FOR RESIDUE MG D 422
05
AC5
SOFTWARE
ARG C:39 , LYS C:219 , GLY C:375 , GLY C:376 , GLY C:398 , ADP C:421 , MG C:422 , HOH C:759
BINDING SITE FOR RESIDUE PO4 C 624
06
AC6
SOFTWARE
ARG D:39 , LYS D:219 , GLY D:375 , GLY D:376 , GLY D:398 , ADP D:421 , MG D:422 , HOH D:747
BINDING SITE FOR RESIDUE PO4 D 625
07
AC7
SOFTWARE
LEU A:103 , ARG A:105 , PHE D:344 , GLU D:345 , LEU D:384
BINDING SITE FOR RESIDUE PO4 A 701
08
AC8
SOFTWARE
LYS B:48 , LEU B:103 , PHE C:354 , LEU C:384 , HOH C:789
BINDING SITE FOR RESIDUE PO4 C 702
09
AC9
SOFTWARE
PHE B:344 , VAL B:347 , LEU B:384 , LEU C:103 , ARG C:105
BINDING SITE FOR RESIDUE PO4 C 703
10
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
11
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
12
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
13
BC4
SOFTWARE
GLY B:217 , ALA B:218 , LYS B:219 , LYS B:223 , GLY B:241 , ALA B:242 , TYR B:245 , ALA B:314 , LEU B:315 , ASN B:338 , PRO B:340 , GLY B:342 , VAL B:343 , GLU B:345 , GLY B:375 , GLY B:376 , ASP B:377 , SER B:378 , MG B:422 , HOH B:430 , HOH B:442 , HOH B:556 , HOH B:579
BINDING SITE FOR RESIDUE ADP B 421
14
BC5
SOFTWARE
ASP B:24 , ASN B:26 , ARG B:39 , HIS B:62 , GLY B:64 , ARG B:65 , ARG B:135 , GLY B:168 , ARG B:172 , LYS B:219 , GLY B:398 , HOH B:480 , HOH B:556
BINDING SITE FOR RESIDUE 3PG B 423
15
BC6
SOFTWARE
GLY C:217 , ALA C:218 , LYS C:219 , LYS C:223 , GLY C:241 , ALA C:242 , TYR C:245 , ALA C:314 , ASN C:338 , PRO C:340 , GLY C:342 , VAL C:343 , GLU C:345 , GLY C:375 , GLY C:376 , ASP C:377 , SER C:378 , MG C:422 , PO4 C:624
BINDING SITE FOR RESIDUE ADP C 421
16
BC7
SOFTWARE
GLY D:217 , ALA D:218 , LYS D:219 , LYS D:223 , GLY D:241 , ALA D:242 , TYR D:245 , ALA D:314 , ASN D:338 , GLY D:339 , PRO D:340 , GLY D:342 , VAL D:343 , GLU D:345 , GLY D:375 , GLY D:376 , ASP D:377 , SER D:378 , MG D:422 , PO4 D:625 , HOH D:654
BINDING SITE FOR RESIDUE ADP D 421
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_PGKC_TRYBB_001 (G75D, chain A/B/C/D, )
View:
Select:
Label:
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/B/C/D
G
75
D
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PGLYCERATE_KINASE (A:18-28,B:18-28,C:18-28,D:18-28)
;
View:
Select:
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
4
A:18-28
B:18-28
C:18-28
D:18-28
[
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]
Exons
(0, 0)
Info
All Exons
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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
(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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(
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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
:
Phosphoglycerate kinase
(16)
Trypanosome (Trypanosoma brucei) [TaxId: 5691]
(2)
1a
d13pka_
A:
1b
d13pkb_
B:
1c
d13pkc_
C:
1d
d13pkd_
D:
[
close SCOP info
]
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
(
)
(
)
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)
Info
all PFAM domains
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Asymmetric Unit 1
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