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3MOH
Asym. Unit
Info
Asym.Unit (222 KB)
Biol.Unit 1 (107 KB)
Biol.Unit 2 (107 KB)
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(1)
Title
:
THE STRUCTURE OF RAT CYTOSOLIC PEPCK MUTANT A467G IN COMPLEX WITH PHOSPHOGLYCOLATE AND GDP
Authors
:
T. A. Johnson, T. Holyoak
Date
:
22 Apr 10 (Deposition) - 02 Jun 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Kinase, Gluconeogenesis, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. A. Johnson, T. Holyoak
Increasing The Conformational Entropy Of The Omega-Loop Lid Domain In Phosphoenolpyruvate Carboxykinase Impairs Catalysis And Decreases Catalytic Fidelity .
Biochemistry V. 49 5176 2010
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Hetero Components
(6, 13)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
2a: 1,2-ETHANEDIOL (EDOa)
3a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
3b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
4c: MANGANESE (II) ION (MNc)
4d: MANGANESE (II) ION (MNd)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
6a: 2-PHOSPHOGLYCOLIC ACID (PGAa)
6b: 2-PHOSPHOGLYCOLIC ACID (PGAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
GDP
2
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
4
MN
4
Ligand/Ion
MANGANESE (II) ION
5
NA
2
Ligand/Ion
SODIUM ION
6
PGA
2
Ligand/Ion
2-PHOSPHOGLYCOLIC ACID
[
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:285 , SER A:286 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533 , HOH A:624 , HOH A:625 , HOH A:640 , MN A:701 , HOH A:748 , HOH A:767 , HOH A:782 , HOH A:803 , HOH A:859 , HOH A:896 , HOH A:991
BINDING SITE FOR RESIDUE GDP A 1000
02
AC2
SOFTWARE
LYS A:244 , HIS A:264 , ASP A:311 , HOH A:623 , PGA A:900 , HOH A:907
BINDING SITE FOR RESIDUE MN A 700
03
AC3
SOFTWARE
THR A:291 , ASP A:310 , HOH A:624 , HOH A:625 , HOH A:767 , HOH A:893 , GDP A:1000
BINDING SITE FOR RESIDUE MN A 701
04
AC4
SOFTWARE
ARG A:87 , GLY A:237 , LYS A:244 , ASP A:311 , PHE A:333 , ARG A:405 , HOH A:623 , MN A:700 , HOH A:740 , HOH A:750 , HOH A:767 , HOH A:907 , HOH A:937
BINDING SITE FOR RESIDUE PGA A 900
05
AC5
SOFTWARE
LEU A:79 , ASN A:208 , HOH A:721 , HOH A:820
BINDING SITE FOR RESIDUE NA A 1100
06
AC6
SOFTWARE
ALA A:128
BINDING SITE FOR RESIDUE EDO A 1200
07
AC7
SOFTWARE
ALA A:447 , SER A:449 , TRP A:450 , PRO A:509 , LYS A:510 , ILE A:511 , HOH A:953
BINDING SITE FOR RESIDUE 1PE A 1300
08
AC8
SOFTWARE
PRO B:285 , SER B:286 , ALA B:287 , 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 , HOH B:640 , HOH B:667 , MN B:701 , HOH B:733 , HOH B:739 , HOH B:746 , HOH B:785 , HOH B:840 , HOH B:863
BINDING SITE FOR RESIDUE GDP B 1000
09
AC9
SOFTWARE
LYS B:244 , HIS B:264 , ASP B:311 , HOH B:639 , HOH B:845 , PGA B:900
BINDING SITE FOR RESIDUE MN B 700
10
BC1
SOFTWARE
THR B:291 , HOH B:640 , HOH B:746 , HOH B:840 , HOH B:841 , GDP B:1000
BINDING SITE FOR RESIDUE MN B 701
11
BC2
SOFTWARE
ARG B:87 , GLY B:237 , LYS B:244 , SER B:286 , ASP B:311 , ARG B:405 , HOH B:639 , MN B:700 , HOH B:845
BINDING SITE FOR RESIDUE PGA B 900
12
BC3
SOFTWARE
VAL B:65 , LEU B:79 , ASN B:208 , HOH B:816 , HOH B:817
BINDING SITE FOR RESIDUE NA B 1100
13
BC4
SOFTWARE
LYS B:14 , GLN B:39 , HOH B:633
BINDING SITE FOR RESIDUE 1PE B 1300
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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:12-75 | 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:440-465 | B:440-465)
Exon 1.10 (A:473-622 | 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:
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:12-75
B:3-75
64
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:440-465
B:440-465
26
26
1.10
ENSRNOT00000031586
10
ENSRNOE00000271120
chr3:
164017282-164018345
1064
PCKGC_RAT
472-622
151
2
A:473-622
B:473-622
150
150
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3moha1 (A:12-259)
1b: SCOP_d3mohb1 (B:3-259)
2a: SCOP_d3moha2 (A:260-622)
2b: SCOP_d3mohb2 (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
d3moha1
A:12-259
1b
d3mohb1
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
d3moha2
A:260-622
2b
d3mohb2
B:260-622
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PEPCK_3mohB01 (B:29-622)
1b: PFAM_PEPCK_3mohB02 (B:29-622)
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Clans
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(
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(
)
Clan
:
PEP-carboxyk
(36)
Family
:
PEPCK
(19)
Rattus norvegicus (Rat)
(11)
1a
PEPCK-3mohB01
B:29-622
1b
PEPCK-3mohB02
B:29-622
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