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3DTB
Biol. Unit 2
Info
Asym.Unit (244 KB)
Biol.Unit 1 (122 KB)
Biol.Unit 2 (119 KB)
Biol.Unit 3 (235 KB)
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(1)
Title
:
THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH PHOSPHOGLYCOLATE AND GDP
Authors
:
S. M. Sullivan, T. Holyoak
Date
:
14 Jul 08 (Deposition) - 26 Aug 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Kinase, Gluconeogenesis, Lyase, Decarboxylase, Gtp-Binding, Nucleotide-Binding
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. M. Sullivan, T. Holyoak
Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead Of Conformational Selection.
Proc. Natl. Acad. Sci. Usa V. 105 13829 2008
[
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
2a: BICARBONATE ION (BCTa)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
4b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
5c: MANGANESE (II) ION (MNc)
5d: MANGANESE (II) ION (MNd)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
7a: 2-PHOSPHOGLYCOLIC ACID (PGAa)
7b: 2-PHOSPHOGLYCOLIC ACID (PGAb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
1PE
-1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
BCT
-1
Ligand/Ion
BICARBONATE ION
3
EPE
-1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
5
MN
-1
Ligand/Ion
MANGANESE (II) ION
6
NA
-1
Ligand/Ion
SODIUM ION
7
PGA
1
Ligand/Ion
2-PHOSPHOGLYCOLIC ACID
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Sites
(6, 6)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC3 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ARG B:87 , GLY B:236 , GLY B:237 , LYS B:244 , ASP B:311 , ARG B:405
BINDING SITE FOR RESIDUE PGA B 900
2
AC6
SOFTWARE
LYS B:244 , HIS B:264 , ASP B:311
BINDING SITE FOR RESIDUE MN B 700
3
AC7
SOFTWARE
THR B:291
BINDING SITE FOR RESIDUE MN B 701
4
AC8
SOFTWARE
LEU B:79 , ASN B:208
BINDING SITE FOR RESIDUE NA B 1100
5
AC9
SOFTWARE
ILE A:95 , LEU A:222 , PRO A:223 , ASP A:224 , ARG A:225 , GLY B:570
BINDING SITE FOR RESIDUE BCT A 1044
6
BC3
SOFTWARE
PRO B:285 , ALA B:287 , CYS B:288 , GLY B:289 , LYS B:290 , THR B:291 , ASN B:292 , ARG B:436 , TRP B:516 , PHE B:517 , PHE B:525 , GLY B:529 , PHE B:530 , ASN B:533
BINDING SITE FOR RESIDUE GDP B 800
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SAPs(SNPs)/Variants
(0, 0)
Info
(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)
;
View:
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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)
Info
All Exons
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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_d3dtba1 (A:3-259)
1b: SCOP_d3dtbb1 (B:3-259)
2a: SCOP_d3dtba2 (A:260-622)
2b: SCOP_d3dtbb2 (B:260-622)
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)
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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
d3dtba1
A:3-259
1b
d3dtbb1
B:3-259
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
d3dtba2
A:260-622
2b
d3dtbb2
B:260-622
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_3dtbA01 (A:11-64,A:88-259)
1b: CATH_3dtbB01 (B:10-64,B:88-259)
2a: CATH_3dtbB03 (B:260-329,B:415-622)
2b: CATH_3dtbA03 (A:260-329,A:415-622)
3a: CATH_3dtbA02 (A:65-87,A:330-414)
3b: CATH_3dtbB02 (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)
Brown rat,rat,rats (Rattus norvegicus)
(4)
1a
3dtbA01
A:11-64,A:88-259
1b
3dtbB01
B:10-64,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)
Brown rat,rat,rats (Rattus norvegicus)
(4)
2a
3dtbB03
B:260-329,B:415-622
2b
3dtbA03
A:260-329,A:415-622
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 2
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 2
(42)
Brown rat,rat,rats (Rattus norvegicus)
(4)
3a
3dtbA02
A:65-87,A:330-414
3b
3dtbB02
B:65-87,B:330-414
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Pfam Domains
(0, 0)
Info
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Chain B
Asymmetric Unit 1
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Asym.Unit (244 KB)
Header - Asym.Unit
Biol.Unit 1 (122 KB)
Header - Biol.Unit 1
Biol.Unit 2 (119 KB)
Header - Biol.Unit 2
Biol.Unit 3 (235 KB)
Header - Biol.Unit 3
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