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3DTB
Asym. Unit
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:
[
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
[
close entry info
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Hetero Components
(7, 14)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
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
2
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
5
MN
4
Ligand/Ion
MANGANESE (II) ION
6
NA
2
Ligand/Ion
SODIUM ION
7
PGA
2
Ligand/Ion
2-PHOSPHOGLYCOLIC ACID
[
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Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:87 , LYS A:244 , HIS A:264 , SER A:286 , ALA A:287 , LYS A:290 , ASP A:311 , ARG A:405 , PHE A:485
BINDING SITE FOR RESIDUE PGA A 900
02
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
03
AC3
SOFTWARE
LYS A:244 , HIS A:264 , ASP A:311
BINDING SITE FOR RESIDUE MN A 700
04
AC4
SOFTWARE
THR A:291
BINDING SITE FOR RESIDUE MN A 701
05
AC5
SOFTWARE
LEU A:79 , ASN A:208
BINDING SITE FOR RESIDUE NA A 1100
06
AC6
SOFTWARE
LYS B:244 , HIS B:264 , ASP B:311
BINDING SITE FOR RESIDUE MN B 700
07
AC7
SOFTWARE
THR B:291
BINDING SITE FOR RESIDUE MN B 701
08
AC8
SOFTWARE
LEU B:79 , ASN B:208
BINDING SITE FOR RESIDUE NA B 1100
09
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
10
BC1
SOFTWARE
PRO A:285 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , PRO A:337 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533
BINDING SITE FOR RESIDUE GDP A 800
11
BC2
SOFTWARE
LEU A:153 , TRP A:260 , LYS A:316 , ARG A:324 , GLU A:424
BINDING SITE FOR RESIDUE 1PE A 1000
12
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
13
BC4
SOFTWARE
ASN A:7 , ASP A:10 , ALA A:13 , LYS A:14 , GLN A:39
BINDING SITE FOR RESIDUE 1PE A 1101
14
BC5
SOFTWARE
PHE A:30 , ASN A:34 , GLU A:123 , PHE A:126 , LYS A:191 , GLU A:227 , ILE A:229
BINDING SITE FOR RESIDUE EPE A 3380
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PEPCK_GTP (A:284-292,B:284-292)
;
View:
Select:
Label:
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
2
A:284-292
B:284-292
[
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]
Exons
(9, 18)
Info
All Exons
Exon 1.2 (A:3-75 | B:3-75)
Exon 1.3 (A:75-136 | B:75-136)
Exon 1.4 (A:136-204 | B:136-204)
Exon 1.5 (A:204-266 | B:204-266)
Exon 1.6 (A:267-321 | B:267-321)
Exon 1.7 (A:321-396 | B:321-396)
Exon 1.8 (A:396-440 | B:396-440)
Exon 1.9 (A:440-472 | B:440-464)
Exon 1.10 (A:472-622 | B:473-622)
View:
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All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/-
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENSRNOT00000031586
1
ENSRNOE00000330605
chr3:
164012410-164012511
102
PCKGC_RAT
-
0
0
-
-
1.2
ENSRNOT00000031586
2
ENSRNOE00000271129
chr3:
164012684-164012948
265
PCKGC_RAT
1-75
75
2
A:3-75
B:3-75
73
73
1.3
ENSRNOT00000031586
3
ENSRNOE00000271110
chr3:
164013321-164013502
182
PCKGC_RAT
75-136
62
2
A:75-136
B:75-136
62
62
1.4
ENSRNOT00000031586
4
ENSRNOE00000271108
chr3:
164014063-164014266
204
PCKGC_RAT
136-204
69
2
A:136-204
B:136-204
69
69
1.5
ENSRNOT00000031586
5
ENSRNOE00000271105
chr3:
164014535-164014722
188
PCKGC_RAT
204-266
63
2
A:204-266
B:204-266
63
63
1.6
ENSRNOT00000031586
6
ENSRNOE00000271102
chr3:
164015301-164015463
163
PCKGC_RAT
267-321
55
2
A:267-321
B:267-321
55
55
1.7
ENSRNOT00000031586
7
ENSRNOE00000271098
chr3:
164016073-164016297
225
PCKGC_RAT
321-396
76
2
A:321-396
B:321-396
76
76
1.8
ENSRNOT00000031586
8
ENSRNOE00000271095
chr3:
164016388-164016519
132
PCKGC_RAT
396-440
45
2
A:396-440
B:396-440
45
45
1.9
ENSRNOT00000031586
9
ENSRNOE00000271092
chr3:
164017053-164017148
96
PCKGC_RAT
440-472
33
2
A:440-472
B:440-464
33
25
1.10
ENSRNOT00000031586
10
ENSRNOE00000271120
chr3:
164017282-164018345
1064
PCKGC_RAT
472-622
151
2
A:472-622
B:473-622
151
150
[
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]
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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)
(
)
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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(
)
(
)
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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
all PFAM domains
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