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2RK7
Biol. Unit 2
Info
Asym.Unit (227 KB)
Biol.Unit 1 (111 KB)
Biol.Unit 2 (111 KB)
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(1)
Title
:
THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH OXALATE
Authors
:
S. M. Sullivan, R. M. Stiffin, G. M. Carlson, T. Holyoak
Date
:
16 Oct 07 (Deposition) - 29 Jan 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Kinase, Gluconeogenesis, Lyase, Decarboxylase, Gtp-Binding, Nucleotide-Binding
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
R. M. Stiffin, S. M. Sullivan, G. M. Carlson, T. Holyoak
Differential Inhibition Of Cytosolic Pepck By Substrate Analogues. Kinetic And Structural Characterization Of Inhibitor Recognition.
Biochemistry V. 47 2099 2008
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
3a: OXALATE ION (OXLa)
3b: OXALATE ION (OXLb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MN
-1
Ligand/Ion
MANGANESE (II) ION
2
NA
-1
Ligand/Ion
SODIUM ION
3
OXL
1
Ligand/Ion
OXALATE ION
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Sites
(4, 4)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
LYS B:244 , HIS B:264 , ASP B:311 , OXL B:5575 , HOH B:5794
BINDING SITE FOR RESIDUE MN B 700
2
AC6
SOFTWARE
VAL B:65 , LEU B:79 , ASN B:208 , HOH B:5645 , HOH B:5726 , HOH B:5939
BINDING SITE FOR RESIDUE NA B 701
3
AC7
SOFTWARE
ARG B:87 , LYS B:244 , HIS B:264 , SER B:286 , ASP B:311 , ARG B:405 , MN B:700 , HOH B:5770 , HOH B:5794
BINDING SITE FOR RESIDUE OXL B 5575
4
AC8
SOFTWARE
PHE B:530 , ASN B:533
BINDING SITE FOR RESIDUE MN B 5576
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PEPCK_GTP (B:284-292)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEPCK_GTP
PS00505
Phosphoenolpyruvate carboxykinase (GTP) signature.
PCKGC_RAT
284-292
1
-
B:284-292
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Exons
(0, 0)
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2rk7a1 (A:4-259)
1b: SCOP_d2rk7b1 (B:4-259)
2a: SCOP_d2rk7a2 (A:260-622)
2b: SCOP_d2rk7b2 (B:260-622)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PEP carboxykinase N-terminal domain
(54)
Superfamily
:
PEP carboxykinase N-terminal domain
(54)
Family
:
PEP carboxykinase N-terminal domain
(48)
Protein domain
:
Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)
(32)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(25)
1a
d2rk7a1
A:4-259
1b
d2rk7b1
B:4-259
Fold
:
PEP carboxykinase-like
(61)
Superfamily
:
PEP carboxykinase-like
(61)
Family
:
PEP carboxykinase C-terminal domain
(48)
Protein domain
:
Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)
(32)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(25)
2a
d2rk7a2
A:260-622
2b
d2rk7b2
B:260-622
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2rk7A01 (A:11-64,A:88-259)
1b: CATH_2rk7B01 (B:11-64,B:88-259)
2a: CATH_2rk7A03 (A:260-329,A:415-622)
2b: CATH_2rk7B03 (B:260-329,B:415-622)
3a: CATH_2rk7A02 (A:65-87,A:330-414)
3b: CATH_2rk7B02 (B:65-87,B:330-414)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 1
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 1
(42)
Norway rat (Rattus norvegicus)
(9)
1a
2rk7A01
A:11-64,A:88-259
1b
2rk7B01
B:11-64,B:88-259
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 3
(62)
Homologous Superfamily
:
[code=3.90.228.20, no name defined]
(42)
Norway rat (Rattus norvegicus)
(9)
2a
2rk7A03
A:260-329,A:415-622
2b
2rk7B03
B:260-329,B:415-622
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 2
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 2
(42)
Norway rat (Rattus norvegicus)
(9)
3a
2rk7A02
A:65-87,A:330-414
3b
2rk7B02
B:65-87,B:330-414
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PEPCK_2rk7B01 (B:29-622)
1b: PFAM_PEPCK_2rk7B02 (B:29-622)
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Clan
:
PEP-carboxyk
(36)
Family
:
PEPCK
(19)
Rattus norvegicus (Rat)
(11)
1a
PEPCK-2rk7B01
B:29-622
1b
PEPCK-2rk7B02
B:29-622
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Chain B
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (227 KB)
Header - Asym.Unit
Biol.Unit 1 (111 KB)
Header - Biol.Unit 1
Biol.Unit 2 (111 KB)
Header - Biol.Unit 2
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