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1ZS6
Asym. Unit
Info
Asym.Unit (81 KB)
Biol.Unit 1 (151 KB)
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(1)
Title
:
STRUCTURE OF HUMAN NUCLEOSIDE-DIPHOSPHATE KINASE 3
Authors
:
J. Choe, S. Dimov, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkare Structural Genomics Consortium (Sgc)
Date
:
23 May 05 (Deposition) - 07 Jun 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,D
Biol. Unit 1: A,B,D (2x)
Keywords
:
Nucleotide Metabolism, Apoptosis, Kinase, Transferase, Structural Genomics, Structural Genomics Consortium, Sgc
(Keyword Search:
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Reference
:
S. Dimov, J. Choe, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkarev, H. Park
Structure Of Human Nucleoside-Diphosphate Kinase 3
To Be Published
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Hetero Components
(1, 3)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
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Label:
No.
Name
Count
Type
Full Name
1
ADP
3
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:29 , PHE A:77 , LEU A:81 , ARG A:105 , THR A:111 , ARG A:122 , VAL A:129 , ASN A:132
BINDING SITE FOR RESIDUE ADP A 201
2
AC2
SOFTWARE
GLU A:169 , LYS B:29 , TYR B:69 , LEU B:72 , PHE B:77 , LEU B:81 , ARG B:105 , THR B:111 , VAL B:129 , GLY B:130 , ASN B:132 , HOH B:301 , LYS D:83
BINDING SITE FOR RESIDUE ADP B 202
3
AC3
SOFTWARE
LYS D:29 , TYR D:69 , LEU D:72 , PHE D:77 , LEU D:81 , ARG D:105 , THR D:111 , ARG D:122 , VAL D:129 , ASN D:132 , HOH D:307 , HOH D:321
BINDING SITE FOR RESIDUE ADP D 203
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: NDP_KINASES (A:132-140,B:132-140,D:132-140)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NDP_KINASES
PS00469
Nucleoside diphosphate kinases active site.
NDK3_HUMAN
132-140
3
A:132-140
B:132-140
D:132-140
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Exons
(4, 12)
Info
All Exons
Exon 1.2 (A:18-59 | B:18-59 | D:18-59)
Exon 1.3 (A:60-93 | B:60-93 | D:60-93)
Exon 1.4 (A:94-131 | B:94-131 | D:94-131)
Exon 1.5 (A:131-169 | B:131-169 | D:131-169)
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/-
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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
1.1
ENST00000219302
1
ENSE00001273366
chr16:
1821710-1821490
221
NDK3_HUMAN
1-16
16
0
-
-
1.2
ENST00000219302
2
ENSE00000683466
chr16:
1821411-1821281
131
NDK3_HUMAN
16-59
44
3
A:18-59
B:18-59
D:18-59
42
42
42
1.3
ENST00000219302
3
ENSE00000683469
chr16:
1821172-1821071
102
NDK3_HUMAN
60-93
34
3
A:60-93
B:60-93
D:60-93
34
34
34
1.4
ENST00000219302
4
ENSE00000683471
chr16:
1820994-1820882
113
NDK3_HUMAN
94-131
38
3
A:94-131
B:94-131
D:94-131
38
38
38
1.5
ENST00000219302
5
ENSE00000892274
chr16:
1820767-1820321
447
NDK3_HUMAN
131-169
39
3
A:131-169
B:131-169
D:131-169
39
39
39
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SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1zs6a1 (A:18-169)
1b: SCOP_d1zs6b_ (B:)
1c: SCOP_d1zs6d_ (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), NDK3 [TaxId: 9606]
(1)
1a
d1zs6a1
A:18-169
1b
d1zs6b_
B:
1c
d1zs6d_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_NDK_1zs6D01 (D:22-156)
1b: PFAM_NDK_1zs6D02 (D:22-156)
1c: PFAM_NDK_1zs6D03 (D:22-156)
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Clan
:
no clan defined [family: NDK]
(40)
Family
:
NDK
(40)
Homo sapiens (Human)
(6)
1a
NDK-1zs6D01
D:22-156
1b
NDK-1zs6D02
D:22-156
1c
NDK-1zs6D03
D:22-156
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Asymmetric Unit 1
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