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2RKA
Asym. Unit
Info
Asym.Unit (231 KB)
Biol.Unit 1 (113 KB)
Biol.Unit 2 (114 KB)
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(1)
Title
:
THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH PHOSPHOGLYCOLATE
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
:
1.95
Chains
:
Asym. Unit : A,C
Biol. Unit 1: A (1x)
Biol. Unit 2: C (1x)
Keywords
:
Kinase, Gluconeogenesis, Lyase, Decarboxylase, Gtp-Binding, Nucleotide-Binding
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
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
(3, 8)
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: 2-PHOSPHOGLYCOLIC ACID (PGAa)
3b: 2-PHOSPHOGLYCOLIC ACID (PGAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
4
Ligand/Ion
MANGANESE (II) ION
2
NA
2
Ligand/Ion
SODIUM ION
3
PGA
2
Ligand/Ion
2-PHOSPHOGLYCOLIC ACID
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:87 , GLY A:236 , GLY A:237 , LYS A:243 , LYS A:244 , ASP A:311 , PHE A:333 , ASN A:403 , ARG A:405 , MN A:700 , HOH A:703 , HOH A:1099 , HOH A:1138
BINDING SITE FOR RESIDUE PGA A 623
2
AC2
SOFTWARE
ALA C:86 , ARG C:87 , TYR C:235 , GLY C:236 , GLY C:237 , LYS C:243 , LYS C:244 , ASP C:311 , PHE C:333 , ASN C:403 , ARG C:405 , PHE C:485 , MN C:700 , HOH C:704 , HOH C:705 , HOH C:987 , HOH C:1114
BINDING SITE FOR RESIDUE PGA C 623
3
AC3
SOFTWARE
LYS A:244 , HIS A:264 , ASP A:311 , PGA A:623 , HOH A:703 , HOH A:704 , HOH A:1138
BINDING SITE FOR RESIDUE MN A 700
4
AC4
SOFTWARE
HIS A:502 , GLU A:607 , HOH A:753 , HOH A:1016 , HOH A:1017
BINDING SITE FOR RESIDUE MN A 701
5
AC5
SOFTWARE
LEU A:79 , ASN A:208 , HOH A:815 , HOH A:914 , HOH A:1021
BINDING SITE FOR RESIDUE NA A 702
6
AC6
SOFTWARE
LYS C:244 , HIS C:264 , ASP C:311 , PGA C:623 , HOH C:703 , HOH C:704 , HOH C:1114
BINDING SITE FOR RESIDUE MN C 700
7
AC7
SOFTWARE
HIS C:502 , GLU C:607 , HOH C:1007
BINDING SITE FOR RESIDUE MN C 701
8
AC8
SOFTWARE
LEU C:79 , ASN C:208 , HOH C:779 , HOH C:791
BINDING SITE FOR RESIDUE NA C 702
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PEPCK_GTP (A:284-292,C: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
C:284-292
[
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Exons
(9, 18)
Info
All Exons
Exon 1.2 (A:4-75 | C:4-75)
Exon 1.3 (A:75-136 | C:75-136)
Exon 1.4 (A:136-204 | C:136-204)
Exon 1.5 (A:204-266 | C:204-266)
Exon 1.6 (A:267-321 | C:267-321)
Exon 1.7 (A:321-396 | C:321-396)
Exon 1.8 (A:396-440 | C:396-440)
Exon 1.9 (A:440-464 | C:440-472 (gaps))
Exon 1.10 (A:473-622 | C:472-622)
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:
Label:
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:4-75
C:4-75
72
72
1.3
ENSRNOT00000031586
3
ENSRNOE00000271110
chr3:
164013321-164013502
182
PCKGC_RAT
75-136
62
2
A:75-136
C:75-136
62
62
1.4
ENSRNOT00000031586
4
ENSRNOE00000271108
chr3:
164014063-164014266
204
PCKGC_RAT
136-204
69
2
A:136-204
C:136-204
69
69
1.5
ENSRNOT00000031586
5
ENSRNOE00000271105
chr3:
164014535-164014722
188
PCKGC_RAT
204-266
63
2
A:204-266
C:204-266
63
63
1.6
ENSRNOT00000031586
6
ENSRNOE00000271102
chr3:
164015301-164015463
163
PCKGC_RAT
267-321
55
2
A:267-321
C:267-321
55
55
1.7
ENSRNOT00000031586
7
ENSRNOE00000271098
chr3:
164016073-164016297
225
PCKGC_RAT
321-396
76
2
A:321-396
C:321-396
76
76
1.8
ENSRNOT00000031586
8
ENSRNOE00000271095
chr3:
164016388-164016519
132
PCKGC_RAT
396-440
45
2
A:396-440
C:396-440
45
45
1.9
ENSRNOT00000031586
9
ENSRNOE00000271092
chr3:
164017053-164017148
96
PCKGC_RAT
440-472
33
2
A:440-464
C:440-472 (gaps)
25
33
1.10
ENSRNOT00000031586
10
ENSRNOE00000271120
chr3:
164017282-164018345
1064
PCKGC_RAT
472-622
151
2
A:473-622
C:472-622
150
151
[
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2rkaa1 (A:4-259)
1b: SCOP_d2rkac1 (C:4-259)
2a: SCOP_d2rkaa2 (A:260-622)
2b: SCOP_d2rkac2 (C: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
d2rkaa1
A:4-259
1b
d2rkac1
C: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
d2rkaa2
A:260-622
2b
d2rkac2
C:260-622
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2rkaA01 (A:11-64,A:88-259)
1b: CATH_2rkaC01 (C:11-64,C:88-259)
2a: CATH_2rkaA03 (A:260-329,A:415-622)
2b: CATH_2rkaC03 (C:260-329,C:415-622)
3a: CATH_2rkaA02 (A:65-87,A:330-414)
3b: CATH_2rkaC02 (C:65-87,C: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
2rkaA01
A:11-64,A:88-259
1b
2rkaC01
C:11-64,C: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
2rkaA03
A:260-329,A:415-622
2b
2rkaC03
C:260-329,C: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
2rkaA02
A:65-87,A:330-414
3b
2rkaC02
C:65-87,C:330-414
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PEPCK_2rkaC01 (C:29-622)
1b: PFAM_PEPCK_2rkaC02 (C:29-622)
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)
Clan
:
PEP-carboxyk
(36)
Family
:
PEPCK
(19)
Rattus norvegicus (Rat)
(11)
1a
PEPCK-2rkaC01
C:29-622
1b
PEPCK-2rkaC02
C:29-622
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Asym.Unit (231 KB)
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