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Asym. Unit
Info
Asym.Unit (106 KB)
Biol.Unit 1 (102 KB)
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(1)
Title
:
PEPCK COMPLEX WITH NONHYDROLYZABLE GTP ANALOG, NATIVE DATA
Authors
:
P. Dunten, C. Belunis, R. Crowther, K. Hollfelder, U. Kammlott, W. Levin, H. Michel, G. B. Ramsey, A. Swain, D. Weber, S. J. Wertheimer
Date
:
29 Nov 01 (Deposition) - 27 Feb 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Gluconeogenesis, P-Loop, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Dunten, C. Belunis, R. Crowther, K. Hollfelder, U. Kammlott, W. Levin, H. Michel, G. B. Ramsey, A. Swain, D. Weber, S. J. Wertheimer
Crystal Structure Of Human Cytosolic Phosphoenolpyruvate Carboxykinase Reveals A New Gtp-Binding Site.
J. Mol. Biol. V. 316 257 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 6)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (GCPa)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
GCP
1
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
4
MN
2
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:291 , GCP A:704 , HOH A:788 , HOH A:804 , HOH A:805
BINDING SITE FOR RESIDUE MN A 701
2
AC2
SOFTWARE
LYS A:244 , HIS A:264 , ASP A:311 , GCP A:704
BINDING SITE FOR RESIDUE MN A 702
3
AC3
SOFTWARE
ARG A:87 , TYR A:235 , LYS A:244
BINDING SITE FOR RESIDUE ACT A 703
4
AC4
SOFTWARE
ALA A:287 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , ASP A:311 , VAL A:335 , ARG A:405 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533 , MN A:701 , MN A:702 , HOH A:731 , HOH A:732 , HOH A:737 , HOH A:787 , HOH A:788 , HOH A:805 , HOH A:845
BINDING SITE FOR RESIDUE GCP A 704
5
AC5
SOFTWARE
SER A:449 , TRP A:450 , PRO A:509 , LYS A:510 , ILE A:511 , HOH A:876 , HOH A:923
BINDING SITE FOR RESIDUE EDO A 705
6
AC6
SOFTWARE
TYR A:72 , ILE A:348 , GLN A:352 , HOH A:733
BINDING SITE FOR RESIDUE EDO A 706
[
close Site info
]
SAPs(SNPs)/Variants
(9, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_021072 (R55Q, chain A, )
2: VAR_021073 (M60T, chain A, )
3: VAR_021074 (T138I, chain A, )
4: VAR_021075 (L184L, chain A, )
5: VAR_015575 (V267V, chain A, )
6: VAR_021076 (E276K, chain A, )
7: VAR_021077 (V368I, chain A, )
8: VAR_021078 (P427S, chain A, )
9: VAR_042444 (D586D, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021072
R
55
Q
PCKGC_HUMAN
Polymorphism
28383585
A
R
55
Q
2
UniProt
VAR_021073
M
60
T
PCKGC_HUMAN
Polymorphism
28383586
A
M
60
T
3
UniProt
VAR_021074
T
138
I
PCKGC_HUMAN
Polymorphism
28359542
A
T
138
I
4
UniProt
VAR_021075
V
184
L
PCKGC_HUMAN
Polymorphism
707555
A
L
184
L
5
UniProt
VAR_015575
I
267
V
PCKGC_HUMAN
Polymorphism
8192708
A
V
267
V
6
UniProt
VAR_021076
E
276
K
PCKGC_HUMAN
Polymorphism
11552145
A
E
276
K
7
UniProt
VAR_021077
V
368
I
PCKGC_HUMAN
Polymorphism
1804160
A
V
368
I
8
UniProt
VAR_021078
P
427
S
PCKGC_HUMAN
Polymorphism
28359550
A
P
427
S
9
UniProt
VAR_042444
E
586
D
PCKGC_HUMAN
Polymorphism
1042529
A
D
586
D
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PEPCK_GTP (A: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_HUMAN
284-292
1
A:284-292
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.1d (A:10-75)
Exon 1.1f (A:75-136)
Exon 1.1h (A:136-204)
Exon 1.1j (A:204-266)
Exon 1.1m (A:267-321)
Exon 1.1o (A:321-396)
Exon 1.1p (A:396-440)
Exon 1.1q (A:440-464)
Exon 1.2c (A:473-622 (gaps))
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.1d
02: Boundary 1.1d/1.1f
03: Boundary 1.1f/1.1h
04: Boundary 1.1h/1.1j
05: Boundary 1.1j/1.1m
06: Boundary 1.1m/1.1o
07: Boundary 1.1o/1.1p
08: Boundary 1.1p/1.1q
09: Boundary 1.1q/1.2c
10: Boundary 1.2c/-
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
1.1a
ENST00000319441
1a
ENSE00001170096
chr20:
56136136-56136259
124
PCKGC_HUMAN
-
0
0
-
-
1.1d
ENST00000319441
1d
ENSE00000845753
chr20:
56136428-56136691
264
PCKGC_HUMAN
1-75
75
1
A:10-75
66
1.1f
ENST00000319441
1f
ENSE00000845754
chr20:
56137127-56137308
182
PCKGC_HUMAN
75-136
62
1
A:75-136
62
1.1h
ENST00000319441
1h
ENSE00000845755
chr20:
56137752-56137955
204
PCKGC_HUMAN
136-204
69
1
A:136-204
69
1.1j
ENST00000319441
1j
ENSE00000845756
chr20:
56138084-56138271
188
PCKGC_HUMAN
204-266
63
1
A:204-266
63
1.1m
ENST00000319441
1m
ENSE00000845757
chr20:
56138621-56138783
163
PCKGC_HUMAN
267-321
55
1
A:267-321
55
1.1o
ENST00000319441
1o
ENSE00000845758
chr20:
56139225-56139449
225
PCKGC_HUMAN
321-396
76
1
A:321-396
76
1.1p
ENST00000319441
1p
ENSE00000845759
chr20:
56139538-56139669
132
PCKGC_HUMAN
396-440
45
1
A:396-440
45
1.1q
ENST00000319441
1q
ENSE00000845760
chr20:
56140096-56140191
96
PCKGC_HUMAN
440-472
33
1
A:440-464
25
1.2c
ENST00000319441
2c
ENSE00001259794
chr20:
56140406-56141513
1108
PCKGC_HUMAN
472-622
151
1
A:473-622 (gaps)
150
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1khba2 (A:10-259)
2a: SCOP_d1khba1 (A:260-622)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1khba2
A:10-259
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)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d1khba1
A:260-622
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1khbA01 (A:10-63,A:90-258)
2a: CATH_1khbA03 (A:260-330,A:416-620)
3a: CATH_1khbA02 (A:66-85,A:332-413)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 1
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 1
(42)
Human (Homo sapiens)
(7)
1a
1khbA01
A:10-63,A:90-258
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 3
(62)
Homologous Superfamily
:
[code=3.90.228.20, no name defined]
(42)
Human (Homo sapiens)
(7)
2a
1khbA03
A:260-330,A:416-620
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 2
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 2
(42)
Human (Homo sapiens)
(7)
3a
1khbA02
A:66-85,A:332-413
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_PEPCK_1khbA01 (A:29-622)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PEP-carboxyk
(36)
Family
:
PEPCK
(19)
Homo sapiens (Human)
(6)
1a
PEPCK-1khbA01
A:29-622
[
close Pfam info
]
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)
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Protein & NOT Site
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Chain A
Asymmetric Unit 1
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