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1JXV
Asym. Unit
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Asym.Unit (151 KB)
Biol.Unit 1 (148 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A
Authors
:
K. Min, H. K. Song, C. Chang, S. Y. Kim, K. J. Lee, S. W. Suh
Date
:
10 Sep 01 (Deposition) - 10 Apr 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Transferase, Kinase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Min, H. K. Song, C. Chang, S. Y. Kim, K. J. Lee, S. W. Suh
Crystal Structure Of Human Nucleoside Diphosphate Kinase A, A Metastasis Suppressor.
Proteins V. 46 340 2002
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
Info
All Hetero Components
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Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
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Label:
Sorry, no Info available
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SAPs(SNPs)/Variants
(1, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_004625 (S120G, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_004625
S
120
G
NDKA_HUMAN
Polymorphism
121917887
A/B/C/D/E/F
S
120
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: NDP_KINASES (A:115-123,B:115-123,C:115-123,D:11...)
;
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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.
NDKA_HUMAN
115-123
6
A:115-123
B:115-123
C:115-123
D:115-123
E:115-123
F:115-123
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Exons
(4, 24)
Info
All Exons
Exon 1.4b (A:4-42 | B:4-42 | C:4-42 | D:4-42 ...)
Exon 1.5a (A:43-76 | B:43-76 | C:43-76 | D:43...)
Exon 1.6c (A:77-114 | B:77-114 | C:77-114 | D...)
Exon 1.6i (A:114-152 | B:114-152 | C:114-152 ...)
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All Exon Boundaries
1: Boundary 1.1a/1.4b
2: Boundary 1.4b/1.5a
3: Boundary 1.5a/1.6c
4: Boundary 1.6c/1.6i
5: Boundary 1.6i/-
View:
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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
ENST00000393196
1a
ENSE00001874573
chr17:
49230897-49231023
127
NDKA_HUMAN
-
0
0
-
-
1.4b
ENST00000393196
4b
ENSE00002182518
chr17:
49233012-49233141
130
NDKA_HUMAN
1-42
42
6
A:4-42
B:4-42
C:4-42
D:4-42
E:4-42
F:4-42
39
39
39
39
39
39
1.5a
ENST00000393196
5a
ENSE00002174061
chr17:
49237341-49237442
102
NDKA_HUMAN
43-76
34
6
A:43-76
B:43-76
C:43-76
D:43-76
E:43-76
F:43-76
34
34
34
34
34
34
1.6c
ENST00000393196
6c
ENSE00002147222
chr17:
49238521-49238633
113
NDKA_HUMAN
77-114
38
6
A:77-114
B:77-114
C:77-114
D:77-114
E:77-114
F:77-114
38
38
38
38
38
38
1.6i
ENST00000393196
6i
ENSE00001956093
chr17:
49239089-49239556
468
NDKA_HUMAN
114-152
39
6
A:114-152
B:114-152
C:114-152
D:114-152
E:114-152
F:114-152
39
39
39
39
39
39
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SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1jxva_ (A:)
1b: SCOP_d1jxve_ (E:)
1c: SCOP_d1jxvf_ (F:)
1d: SCOP_d1jxvb_ (B:)
1e: SCOP_d1jxvc_ (C:)
1f: SCOP_d1jxvd_ (D:)
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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
:
Nucleoside diphosphate kinase, NDK
(66)
Human (Homo sapiens), NDKA [TaxId: 9606]
(6)
1a
d1jxva_
A:
1b
d1jxve_
E:
1c
d1jxvf_
F:
1d
d1jxvb_
B:
1e
d1jxvc_
C:
1f
d1jxvd_
D:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1jxvA00 (A:4-152)
1b: CATH_1jxvB00 (B:4-152)
1c: CATH_1jxvC00 (C:4-152)
1d: CATH_1jxvD00 (D:4-152)
1e: CATH_1jxvE00 (E:4-152)
1f: CATH_1jxvF00 (F:4-152)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.141, no name defined]
(46)
Human (Homo sapiens)
(5)
1a
1jxvA00
A:4-152
1b
1jxvB00
B:4-152
1c
1jxvC00
C:4-152
1d
1jxvD00
D:4-152
1e
1jxvE00
E:4-152
1f
1jxvF00
F:4-152
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_NDK_1jxvF01 (F:5-139)
1b: PFAM_NDK_1jxvF02 (F:5-139)
1c: PFAM_NDK_1jxvF03 (F:5-139)
1d: PFAM_NDK_1jxvF04 (F:5-139)
1e: PFAM_NDK_1jxvF05 (F:5-139)
1f: PFAM_NDK_1jxvF06 (F:5-139)
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Clan
:
no clan defined [family: NDK]
(40)
Family
:
NDK
(40)
Homo sapiens (Human)
(6)
1a
NDK-1jxvF01
F:5-139
1b
NDK-1jxvF02
F:5-139
1c
NDK-1jxvF03
F:5-139
1d
NDK-1jxvF04
F:5-139
1e
NDK-1jxvF05
F:5-139
1f
NDK-1jxvF06
F:5-139
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Asym.Unit (151 KB)
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