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1UCN
Asym. Unit
Info
Asym.Unit (90 KB)
Biol.Unit 1 (164 KB)
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(1)
Title
:
X-RAY STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A COMPLEXED WITH ADP AT 2 A RESOLUTION
Authors
:
Y. Chen, S. Gallois-Montbrun, B. Schneider, M. Veron, S. Morera, D. Dev Bonne, J. Janin
Date
:
16 Apr 03 (Deposition) - 30 Sep 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Mutant Complexe Adp, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Chen, S. Gallois-Montbrun, B. Schneider, M. Veron, S. Morera, D. Deville-Bonne, J. Janin
Nucleotide Binding To Nucleoside Diphosphate Kinases: X-Ray Structure Of Human Ndpk-A In Complex With Adp And Compariso To Protein Kinases
J. Mol. Biol. V. 332 915 2003
[
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Hetero Components
(4, 12)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
4a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
3
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CA
5
Ligand/Ion
CALCIUM ION
3
PO4
3
Ligand/Ion
PHOSPHATE ION
4
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:10 , LYS A:12 , HIS A:51 , TYR A:52 , GLY A:118 , GLY A:119 , CA A:1162 , HOH A:1226
BINDING SITE FOR RESIDUE PO4 A 1161
02
AC2
SOFTWARE
GLY A:119 , ASP A:121 , ADP A:1160 , PO4 A:1161 , HOH A:1192 , HOH A:1226
BINDING SITE FOR RESIDUE CA A 1162
03
AC3
SOFTWARE
LYS B:12 , HIS B:51 , TYR B:52 , GLY B:118 , GLY B:119 , HOH B:2236 , HOH B:2261
BINDING SITE FOR RESIDUE PO4 B 2161
04
AC4
SOFTWARE
GLY B:119 , ADP B:2160 , HOH B:2236 , HOH B:2261
BINDING SITE FOR RESIDUE CA B 2162
05
AC5
SOFTWARE
HIS C:51 , TYR C:52 , GLY C:118 , GLY C:119 , HOH C:3223
BINDING SITE FOR RESIDUE PO4 C 3161
06
AC6
SOFTWARE
ADP C:3160 , HOH C:3223 , HOH C:3224
BINDING SITE FOR RESIDUE CA C 3162
07
AC7
SOFTWARE
GLY C:131 , HOH C:3204 , HOH C:3205 , HOH C:3206
BINDING SITE FOR RESIDUE CA C 1001
08
AC8
SOFTWARE
GLY B:131 , PHE B:134 , HOH B:2241 , HOH B:2289 , HOH B:2313 , HOH B:2314
BINDING SITE FOR RESIDUE CA B 1002
09
AC9
SOFTWARE
LYS A:12 , LEU A:55 , TRP A:60 , LEU A:64 , ARG A:88 , THR A:94 , ARG A:105 , VAL A:112 , ASN A:115 , ASP A:121 , CA A:1162 , HOH A:1190
BINDING SITE FOR RESIDUE ADP A 1160
10
BC1
SOFTWARE
LYS B:12 , LEU B:55 , TRP B:60 , ARG B:88 , THR B:94 , ARG B:105 , VAL B:112 , ASN B:115 , CA B:2162 , HOH B:2211 , HOH B:2261
BINDING SITE FOR RESIDUE ADP B 2160
11
BC2
SOFTWARE
LYS C:12 , TRP C:60 , LEU C:64 , ARG C:88 , THR C:94 , ARG C:105 , VAL C:112 , ASN C:115 , CA C:3162 , HOH C:3223
BINDING SITE FOR RESIDUE ADP C 3160
12
BC3
SOFTWARE
GLU B:152 , HOH B:2312 , GLU C:152
BINDING SITE FOR RESIDUE TRS B 1003
[
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SAPs(SNPs)/Variants
(1, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_004625 (S120G, chain A/B/C, )
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
S
120
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: NDP_KINASES (A:115-123,B:115-123,C:115-123)
;
View:
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Label:
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
3
A:115-123
B:115-123
C:115-123
[
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]
Exons
(4, 12)
Info
All Exons
Exon 1.4b (A:2-42 | B:2-42 | C:2-42)
Exon 1.5a (A:43-76 | B:43-76 | C:43-76)
Exon 1.6c (A:77-114 | B:77-114 | C:77-114)
Exon 1.6i (A:114-152 | B:114-152 | C:114-152)
View:
Select:
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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:
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
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
3
A:2-42
B:2-42
C:2-42
41
41
41
1.5a
ENST00000393196
5a
ENSE00002174061
chr17:
49237341-49237442
102
NDKA_HUMAN
43-76
34
3
A:43-76
B:43-76
C:43-76
34
34
34
1.6c
ENST00000393196
6c
ENSE00002147222
chr17:
49238521-49238633
113
NDKA_HUMAN
77-114
38
3
A:77-114
B:77-114
C:77-114
38
38
38
1.6i
ENST00000393196
6i
ENSE00001956093
chr17:
49239089-49239556
468
NDKA_HUMAN
114-152
39
3
A:114-152
B:114-152
C:114-152
39
39
39
[
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SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1ucna_ (A:)
1b: SCOP_d1ucnb_ (B:)
1c: SCOP_d1ucnc_ (C:)
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(
)
Organisms
(
)
(
)
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
d1ucna_
A:
1b
d1ucnb_
B:
1c
d1ucnc_
C:
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1ucnA00 (A:2-152)
1b: CATH_1ucnB00 (B:2-152)
1c: CATH_1ucnC00 (C:2-152)
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)
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)
(
)
Organisms
(
)
(
)
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
1ucnA00
A:2-152
1b
1ucnB00
B:2-152
1c
1ucnC00
C:2-152
[
close CATH info
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Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_NDK_1ucnC01 (C:5-139)
1b: PFAM_NDK_1ucnC02 (C:5-139)
1c: PFAM_NDK_1ucnC03 (C:5-139)
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(
)
Clan
:
no clan defined [family: NDK]
(40)
Family
:
NDK
(40)
Homo sapiens (Human)
(6)
1a
NDK-1ucnC01
C:5-139
1b
NDK-1ucnC02
C:5-139
1c
NDK-1ucnC03
C:5-139
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