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2V4Y
Asym. Unit
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Asym.Unit (230 KB)
Biol.Unit 1 (223 KB)
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(1)
Title
:
THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERIC REGULATOR GTP
Authors
:
P. Meyer, C. Evrin, P. Briozzo, N. Joly, O. Barzu, A. M. Gilles
Date
:
30 Sep 08 (Deposition) - 21 Oct 08 (Release) - 16 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Nucleotide-Binding, Pyrimidine Biosynthesis, Transferase, Atp-Binding, Allosteric Enzyme, Gtp, Kinase, Allostery, Nmp Kinase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
P. Meyer, C. Evrin, P. Briozzo, N. Joly, O. Barzu, A. M. Gilles
Structural And Functional Characterization Of Escherichia Coli Ump Kinase In Complex With Its Allosteric Regulator Gtp.
J. Biol. Chem. V. 283 36011 2008
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Hetero Components
(1, 12)
Info
All Hetero Components
1a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
1b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
1c: GUANOSINE-5'-TRIPHOSPHATE (GTPc)
1d: GUANOSINE-5'-TRIPHOSPHATE (GTPd)
1e: GUANOSINE-5'-TRIPHOSPHATE (GTPe)
1f: GUANOSINE-5'-TRIPHOSPHATE (GTPf)
1g: GUANOSINE-5'-TRIPHOSPHATE (GTPg)
1h: GUANOSINE-5'-TRIPHOSPHATE (GTPh)
1i: GUANOSINE-5'-TRIPHOSPHATE (GTPi)
1j: GUANOSINE-5'-TRIPHOSPHATE (GTPj)
1k: GUANOSINE-5'-TRIPHOSPHATE (GTPk)
1l: GUANOSINE-5'-TRIPHOSPHATE (GTPl)
View:
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Label:
No.
Name
Count
Type
Full Name
1
GTP
12
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
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Sites
(12, 12)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:92 , ASP A:93 , HIS A:96 , ASN A:101 , ALA A:102 , ARG A:103 , ARG A:130 , TRP E:119 , ALA E:120 , SER E:124 , ARG E:127 , ASN F:72 , VAL F:75
BINDING SITE FOR RESIDUE GTP A1242
02
AC2
SOFTWARE
TRP A:119 , ALA A:120 , SER A:124 , ARG A:127 , ARG B:92 , ASP B:93 , HIS B:96 , ASN B:101 , ALA B:102 , ARG B:103 , ARG B:130 , ASN D:72 , VAL D:75
BINDING SITE FOR RESIDUE GTP B1242
03
AC3
SOFTWARE
LYS B:6 , ARG C:92 , ASP C:93 , HIS C:96 , ASN C:101 , ALA C:102 , ARG C:103 , ARG C:130 , ASN E:72 , VAL E:75 , TRP F:119 , ALA F:120 , SER F:124 , ARG F:127
BINDING SITE FOR RESIDUE GTP C1242
04
AC4
SOFTWARE
ASN B:72 , VAL B:75 , TRP C:119 , ALA C:120 , SER C:124 , ARG C:127 , ARG D:92 , ASP D:93 , HIS D:96 , ASN D:101 , ALA D:102 , ARG D:103 , ARG D:130
BINDING SITE FOR RESIDUE GTP D1242
05
AC5
SOFTWARE
TRP B:119 , ALA B:120 , SER B:124 , ARG B:127 , ASN C:72 , VAL C:75 , ARG E:92 , ASP E:93 , HIS E:96 , ASN E:101 , ALA E:102 , ARG E:103 , ARG E:130 , LYS F:6
BINDING SITE FOR RESIDUE GTP E1242
06
AC6
SOFTWARE
ASN A:72 , TRP D:119 , ALA D:120 , SER D:124 , ARG D:127 , ARG F:92 , ASP F:93 , HIS F:96 , ASN F:101 , ALA F:102 , ARG F:103 , ARG F:130
BINDING SITE FOR RESIDUE GTP F1242
07
AC7
SOFTWARE
SER F:17 , GLY F:18 , GLU F:19 , GLY F:56 , GLY F:57 , GLY F:58 , THR F:144 , THR F:145
BINDING SITE FOR RESIDUE GTP F1243
08
AC8
SOFTWARE
SER A:17 , GLY A:18 , GLU A:19 , GLY A:56 , GLY A:57 , GLY A:58 , THR A:144 , THR A:145
BINDING SITE FOR RESIDUE GTP A1243
09
AC9
SOFTWARE
SER B:17 , GLY B:18 , GLU B:19 , GLY B:56 , GLY B:57 , GLY B:58 , THR B:144 , THR B:145 , HOH B:2003
BINDING SITE FOR RESIDUE GTP B1243
10
BC1
SOFTWARE
SER D:17 , GLY D:18 , GLU D:19 , GLY D:56 , GLY D:57 , GLY D:58 , THR D:144 , THR D:145 , HOH D:2003
BINDING SITE FOR RESIDUE GTP D1243
11
BC2
SOFTWARE
SER C:17 , GLY C:18 , GLU C:19 , GLY C:56 , GLY C:57 , GLY C:58 , THR C:144 , THR C:145
BINDING SITE FOR RESIDUE GTP C1243
12
BC3
SOFTWARE
SER E:17 , GLY E:18 , GLU E:19 , GLY E:56 , GLY E:57 , GLY E:58 , THR E:144 , THR E:145 , HOH E:2002
BINDING SITE FOR RESIDUE GTP E1243
[
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SAPs(SNPs)/Variants
(2, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_PYRH_ECOLI_001 (R62H, chain A/B/C/D/E/F, )
2: VAR_PYRH_ECOLI_002 (D201N, chain A/B/C/D/E/F, )
View:
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_PYRH_ECOLI_001
*
R
62
H
PYRH_ECOLI
---
---
A/B/C/D/E/F
R
62
H
2
UniProt
VAR_PYRH_ECOLI_002
*
D
201
N
PYRH_ECOLI
---
---
A/B/C/D/E/F
D
201
N
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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Sorry, no Info available
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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.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2v4ya_ (A:)
1b: SCOP_d2v4yb_ (B:)
1c: SCOP_d2v4yc_ (C:)
1d: SCOP_d2v4yd_ (D:)
1e: SCOP_d2v4ye_ (E:)
1f: SCOP_d2v4yf_ (F:)
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Protein Domains
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)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Carbamate kinase-like
(63)
Superfamily
:
Carbamate kinase-like
(63)
Family
:
PyrH-like
(22)
Protein domain
:
automated matches
(11)
Escherichia coli K-12 [TaxId: 83333]
(3)
1a
d2v4ya_
A:
1b
d2v4yb_
B:
1c
d2v4yc_
C:
1d
d2v4yd_
D:
1e
d2v4ye_
E:
1f
d2v4yf_
F:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2v4yA00 (A:5-241)
1b: CATH_2v4yC00 (C:5-241)
1c: CATH_2v4yE00 (E:5-241)
1d: CATH_2v4yD00 (D:5-241)
1e: CATH_2v4yF00 (F:5-241)
1f: CATH_2v4yB00 (B:5-241)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Carbamate kinase
(24)
Homologous Superfamily
:
[code=3.40.1160.10, no name defined]
(24)
Escherichia coli. Organism_taxid: 83333. Strain: k12.
(3)
1a
2v4yA00
A:5-241
1b
2v4yC00
C:5-241
1c
2v4yE00
E:5-241
1d
2v4yD00
D:5-241
1e
2v4yF00
F:5-241
1f
2v4yB00
B:5-241
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_AA_kinase_2v4yF01 (F:10-219)
1b: PFAM_AA_kinase_2v4yF02 (F:10-219)
1c: PFAM_AA_kinase_2v4yF03 (F:10-219)
1d: PFAM_AA_kinase_2v4yF04 (F:10-219)
1e: PFAM_AA_kinase_2v4yF05 (F:10-219)
1f: PFAM_AA_kinase_2v4yF06 (F:10-219)
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Clan
:
no clan defined [family: AA_kinase]
(20)
Family
:
AA_kinase
(20)
Escherichia coli (strain K12)
(5)
1a
AA_kinase-2v4yF01
F:10-219
1b
AA_kinase-2v4yF02
F:10-219
1c
AA_kinase-2v4yF03
F:10-219
1d
AA_kinase-2v4yF04
F:10-219
1e
AA_kinase-2v4yF05
F:10-219
1f
AA_kinase-2v4yF06
F:10-219
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