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1KC7
Biol. Unit 2
Info
Asym.Unit (144 KB)
Biol.Unit 1 (273 KB)
Biol.Unit 2 (273 KB)
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(1)
Title
:
PYRUVATE PHOSPHATE DIKINASE WITH BOUND MG-PHOSPHONOPYRUVATE
Authors
:
C. C. Chen, A. Howard, O. Herzberg
Date
:
07 Nov 01 (Deposition) - 30 Jan 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Biol. Unit 2: A (2x)
Keywords
:
Transferase, Phosphotransferase, Kinase, Phosphonopyruvate Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Herzberg, C. C. Chen, S. Liu, A. Tempczyk, A. Howard, M. Wei, D. Ye, D. Dunaway-Mariano
Pyruvate Site Of Pyruvate Phosphate Dikinase: Crystal Structure Of The Enzyme-Phosphonopyruvate Complex, And Mutant Analysis
Biochemistry V. 41 780 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
2a: PHOSPHONOPYRUVATE (PPRa)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
PPR
2
Ligand/Ion
PHOSPHONOPYRUVATE
3
SO4
8
Ligand/Ion
SULFATE ION
[
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]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:745 , ASP A:769 , PPR A:1000
BINDING SITE FOR RESIDUE MG A 1001
2
AC2
SOFTWARE
LYS A:22 , MET A:99 , PRO A:100 , GLY A:101 , MET A:102 , MET A:103 , ARG A:337
BINDING SITE FOR RESIDUE SO4 A 1002
3
AC3
SOFTWARE
ARG A:523 , TRP A:527
BINDING SITE FOR RESIDUE SO4 A 1003
4
AC4
SOFTWARE
LYS A:718 , GLU A:758 , ARG A:823
BINDING SITE FOR RESIDUE SO4 A 1004
5
AC5
SOFTWARE
PRO A:660 , MET A:661 , ARG A:665
BINDING SITE FOR RESIDUE SO4 A 1005
6
AC6
SOFTWARE
ARG A:561 , ARG A:617 , MET A:743 , GLU A:745 , GLY A:766 , THR A:767 , ASN A:768 , ASP A:769 , GLY A:832 , MG A:1001
BINDING SITE FOR RESIDUE PPR A 1000
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PEP_ENZYMES_PHOS_SITE (A:450-461)
2: PEP_ENZYMES_2 (A:761-779)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEP_ENZYMES_PHOS_SITE
PS00370
PEP-utilizing enzymes phosphorylation site signature.
PPDK_CLOSY
450-461
2
A:450-461
2
PEP_ENZYMES_2
PS00742
PEP-utilizing enzymes signature 2.
PPDK_CLOSY
761-779
2
A:761-779
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Exons
(0, 0)
Info
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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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1kc7a3 (A:2-376)
2a: SCOP_d1kc7a2 (A:377-509)
3a: SCOP_d1kc7a1 (A:510-873)
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)
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)
(
)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
Pyruvate phosphate dikinase, N-terminal domain
(10)
Protein domain
:
Pyruvate phosphate dikinase, N-terminal domain
(10)
Clostridium symbiosum [TaxId: 1512]
(7)
1a
d1kc7a3
A:2-376
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
The swivelling beta/beta/alpha domain
(136)
Superfamily
:
Phosphohistidine domain
(22)
Family
:
Pyruvate phosphate dikinase, central domain
(11)
Protein domain
:
Pyruvate phosphate dikinase, central domain
(11)
Clostridium symbiosum [TaxId: 1512]
(8)
2a
d1kc7a2
A:377-509
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Phosphoenolpyruvate/pyruvate domain
(92)
Family
:
Pyruvate phosphate dikinase, C-terminal domain
(10)
Protein domain
:
Pyruvate phosphate dikinase, C-terminal domain
(10)
Clostridium symbiosum [TaxId: 1512]
(7)
3a
d1kc7a1
A:510-873
[
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CATH Domains
(6, 6)
Info
all CATH domains
1a: CATH_1kc7A06 (A:244-341)
2a: CATH_1kc7A01 (A:2-109,A:199-243)
3a: CATH_1kc7A03 (A:383-507)
4a: CATH_1kc7A04 (A:532-873)
5a: CATH_1kc7A02 (A:342-382,A:510-531)
6a: CATH_1kc7A05 (A:110-198)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
D-amino Acid Aminotransferase; Chain A, domain 1
(175)
Homologous Superfamily
:
ATP-grasp fold, B domain
(118)
Clostridium symbiosum. Organism_taxid: 1512.
(5)
1a
1kc7A06
A:244-341
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Clostridium symbiosum. Organism_taxid: 1512.
(5)
2a
1kc7A01
A:2-109,A:199-243
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
Glucose Oxidase; domain 1
(52)
Homologous Superfamily
:
Phosphohistidine domains of PEP-utilising enzymes
(24)
Clostridium symbiosum. Organism_taxid: 1512.
(5)
3a
1kc7A03
A:383-507
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphoenolpyruvate-binding domains
(67)
Clostridium symbiosum. Organism_taxid: 1512.
(5)
4a
1kc7A04
A:532-873
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Pyruvate Phosphate di-kinase; domain 2
(10)
Homologous Superfamily
:
Pyruvate Phosphate Dikinase, domain 2
(10)
Clostridium symbiosum. Organism_taxid: 1512.
(5)
5a
1kc7A02
A:342-382,A:510-531
Architecture
:
Up-down Bundle
(3216)
Topology
:
Acyl-CoA Binding Protein
(47)
Homologous Superfamily
:
[code=1.20.80.30, no name defined]
(10)
Clostridium symbiosum. Organism_taxid: 1512.
(5)
6a
1kc7A05
A:110-198
[
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]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_PEP_utilizers_C_1kc7A01 (A:515-871)
2a: PFAM_PEP_utilizers_1kc7A02 (A:412-503)
3a: PFAM_PPDK_N_1kc7A03 (A:10-362)
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Clans
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)
(
)
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)
(
)
Organisms
(
)
(
)
Clan
:
PK_TIM
(63)
Family
:
PEP-utilizers_C
(11)
Clostridium symbiosum (Bacteroides symbiosus)
(4)
1a
PEP-utilizers_C-1kc7A01
A:515-871
Clan
:
no clan defined [family: PEP-utilizers]
(11)
Family
:
PEP-utilizers
(11)
Clostridium symbiosum (Bacteroides symbiosus)
(4)
2a
PEP-utilizers-1kc7A02
A:412-503
Clan
:
no clan defined [family: PPDK_N]
(7)
Family
:
PPDK_N
(7)
Clostridium symbiosum (Bacteroides symbiosus)
(4)
3a
PPDK_N-1kc7A03
A:10-362
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Asym.Unit (144 KB)
Header - Asym.Unit
Biol.Unit 1 (273 KB)
Header - Biol.Unit 1
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