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3EIC
Asym. Unit
Info
Asym.Unit (141 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (134 KB)
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(1)
Title
:
X-RAY STRUCTURE OF ACANTHAMOEBA PLOYPHAGA MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH UDP
Authors
:
S. Jeudy, A. Lartigue, J. M. Claverie, C. Abergel
Date
:
15 Sep 08 (Deposition) - 16 Jun 09 (Release) - 25 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,E (2x)
Biol. Unit 2: B,D,F (2x)
Keywords
:
Ndk Phosphotransferase Nucleotide Binding, Atp-Binding, Kinase, Magnesium, Metal-Binding, Nucleotide Metabolism, Nucleotide-Binding, Phosphoprotein, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
S. Jeudy, A. Lartigue, J. M. Claverie, C. Abergel
Dissecting The Unique Nucleotide Specificity Of Mimivirus Nucleoside Diphosphate Kinase.
J. Virol. V. 83 7142 2009
(for further references see the
PDB file header
)
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
2a: URIDINE-5'-DIPHOSPHATE (UDPa)
2b: URIDINE-5'-DIPHOSPHATE (UDPb)
2c: URIDINE-5'-DIPHOSPHATE (UDPc)
2d: URIDINE-5'-DIPHOSPHATE (UDPd)
2e: URIDINE-5'-DIPHOSPHATE (UDPe)
2f: URIDINE-5'-DIPHOSPHATE (UDPf)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MG
6
Ligand/Ion
MAGNESIUM ION
2
UDP
6
Ligand/Ion
URIDINE-5'-DIPHOSPHATE
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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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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:86 , UDP A:161
BINDING SITE FOR RESIDUE MG A 160
02
AC2
SOFTWARE
ARG B:86 , UDP B:162
BINDING SITE FOR RESIDUE MG B 161
03
AC3
SOFTWARE
ARG C:86 , UDP C:163
BINDING SITE FOR RESIDUE MG C 162
04
AC4
SOFTWARE
UDP D:164
BINDING SITE FOR RESIDUE MG D 163
05
AC5
SOFTWARE
UDP E:165
BINDING SITE FOR RESIDUE MG E 164
06
AC6
SOFTWARE
ARG F:86 , UDP F:166
BINDING SITE FOR RESIDUE MG F 165
07
AC7
SOFTWARE
LYS A:9 , HIS A:53 , TYR A:58 , ASN A:62 , ARG A:86 , GLN A:89 , ARG A:99 , ILE A:106 , ARG A:107 , ASN A:109 , MG A:160 , HOH A:195 , HOH A:196
BINDING SITE FOR RESIDUE UDP A 161
08
AC8
SOFTWARE
LYS B:9 , TYR B:50 , HIS B:53 , TYR B:58 , ASN B:62 , ARG B:86 , ARG B:99 , ILE B:106 , ARG B:107 , ASN B:109 , MG B:161 , HOH B:171
BINDING SITE FOR RESIDUE UDP B 162
09
AC9
SOFTWARE
LYS C:9 , TYR C:50 , HIS C:53 , TYR C:58 , ASN C:62 , ARG C:86 , ARG C:99 , ILE C:106 , ARG C:107 , ASN C:109 , MG C:162 , HOH C:188 , HOH C:207
BINDING SITE FOR RESIDUE UDP C 163
10
BC1
SOFTWARE
LYS D:9 , TYR D:50 , HIS D:53 , TYR D:58 , ASN D:62 , ARG D:86 , GLN D:89 , ARG D:99 , ILE D:106 , ARG D:107 , ASN D:109 , MG D:163 , HOH D:168 , HOH D:198
BINDING SITE FOR RESIDUE UDP D 164
11
BC2
SOFTWARE
LYS E:9 , HIS E:53 , TYR E:58 , ASN E:62 , ARG E:86 , ARG E:99 , ILE E:106 , ARG E:107 , ASN E:109 , MG E:164 , HOH E:171 , HOH E:204
BINDING SITE FOR RESIDUE UDP E 165
12
BC3
SOFTWARE
LYS F:9 , HIS F:53 , TYR F:58 , ASN F:62 , ARG F:86 , ARG F:99 , ILE F:106 , ARG F:107 , ASN F:109 , MG F:165 , HOH F:195
BINDING SITE FOR RESIDUE UDP F 166
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: NDP_KINASES (A:109-117,B:109-117,C:109-117,D:10...)
;
View:
Select:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NDP_KINASES
PS00469
Nucleoside diphosphate kinases active site.
NDK_MIMIV
109-117
6
A:109-117
B:109-117
C:109-117
D:109-117
E:109-117
F:109-117
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Exons
(0, 0)
Info
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All Exon Boundaries
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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_d3eica_ (A:)
1b: SCOP_d3eicb_ (B:)
1c: SCOP_d3eicc_ (C:)
1d: SCOP_d3eicd_ (D:)
1e: SCOP_d3eice_ (E:)
1f: SCOP_d3eicf_ (F:)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Nucleoside diphosphate kinase, NDK
(129)
Family
:
Nucleoside diphosphate kinase, NDK
(112)
Protein domain
:
automated matches
(46)
Acanthamoeba polyphaga mimivirus [TaxId: 212035]
(23)
1a
d3eica_
A:
1b
d3eicb_
B:
1c
d3eicc_
C:
1d
d3eicd_
D:
1e
d3eice_
E:
1f
d3eicf_
F:
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CATH Domains
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (141 KB)
Header - Asym.Unit
Biol.Unit 1 (136 KB)
Header - Biol.Unit 1
Biol.Unit 2 (134 KB)
Header - Biol.Unit 2
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