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2A30
Asym. Unit
Info
Asym.Unit (149 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (73 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH DEOXYCYTIDINE
Authors
:
M. H. Godsey, S. Ort, E. Sabini, M. Konrad, A. Lavie
Date
:
23 Jun 05 (Deposition) - 17 Jan 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.02
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Nucleoside Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. H. Godsey, S. Ort, E. Sabini, M. Konrad, A. Lavie
Structural Basis For The Preference Of Utp Over Atp In Human Deoxycytidine Kinase: Illuminating The Role Of Main-Chain Reorganization.
Biochemistry V. 45 452 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 2'-DEOXYCYTIDINE (DCZa)
2b: 2'-DEOXYCYTIDINE (DCZb)
2c: 2'-DEOXYCYTIDINE (DCZc)
2d: 2'-DEOXYCYTIDINE (DCZd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
DCZ
4
Ligand/Ion
2'-DEOXYCYTIDINE
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:60
BINDING SITE FOR RESIDUE CA A 261
2
AC2
SOFTWARE
ASN C:60
BINDING SITE FOR RESIDUE CA C 261
3
AC3
SOFTWARE
GLU A:53 , TRP A:58 , TYR A:86 , PHE A:96 , GLN A:97 , ARG A:128 , ASP A:133 , PHE A:137 , GLU A:197
BINDING SITE FOR RESIDUE DCZ A 302
4
AC4
SOFTWARE
GLU B:53 , TRP B:58 , TYR B:86 , PHE B:96 , GLN B:97 , ARG B:128 , ASP B:133 , PHE B:137 , GLU B:197
BINDING SITE FOR RESIDUE DCZ B 402
5
AC5
SOFTWARE
ILE C:30 , GLU C:53 , TRP C:58 , TYR C:86 , PHE C:96 , GLN C:97 , ARG C:128 , ASP C:133 , PHE C:137 , GLU C:197 , HOH C:503 , HOH C:509
BINDING SITE FOR RESIDUE DCZ C 502
6
AC6
SOFTWARE
GLU D:53 , TRP D:58 , MET D:85 , TYR D:86 , PHE D:96 , GLN D:97 , ARG D:128 , ASP D:133 , PHE D:137 , GLU D:197 , HOH D:603
BINDING SITE FOR RESIDUE DCZ D 602
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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
(0, 0)
Info
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;
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End label:
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Exons
(7, 28)
Info
All Exons
Exon 1.3a (A:20-31 | B:20-31 | C:20-31 | D:20...)
Exon 1.4 (A:31-64 | B:31-64 (gaps) | C:31-64...)
Exon 1.5 (A:80-134 | B:80-134 (gaps) | C:80-...)
Exon 1.6 (A:134-183 | B:134-183 | C:134-183 ...)
Exon 1.7a (A:184-222 | B:184-222 | C:184-222 ...)
Exon 1.8a (A:222-252 (gaps) | B:222-252 (gaps...)
Exon 1.10 (A:253-260 | B:253-260 | C:253-260 ...)
View:
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All Exon Boundaries
1: Boundary -/1.3a
2: Boundary 1.3a/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6
5: Boundary 1.6/1.7a
6: Boundary 1.7a/1.8a
7: Boundary 1.8a/1.10
8: Boundary 1.10/-
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
1.3a
ENST00000286648
3a
ENSE00002041408
chr4:
71859156-71859643
488
DCK_HUMAN
1-31
31
4
A:20-31
B:20-31
C:20-31
D:20-31
12
12
12
12
1.4
ENST00000286648
4
ENSE00001024728
chr4:
71863784-71863899
116
DCK_HUMAN
31-69
39
4
A:31-64
B:31-64 (gaps)
C:31-64
D:31-64
34
34
34
34
1.5
ENST00000286648
5
ENSE00001024734
chr4:
71888084-71888277
194
DCK_HUMAN
70-134
65
4
A:80-134
B:80-134 (gaps)
C:80-134
D:80-134 (gaps)
55
55
55
55
1.6
ENST00000286648
6
ENSE00001024731
chr4:
71889276-71889423
148
DCK_HUMAN
134-183
50
4
A:134-183
B:134-183
C:134-183
D:134-183
50
50
50
50
1.7a
ENST00000286648
7a
ENSE00001024724
chr4:
71891533-71891648
116
DCK_HUMAN
184-222
39
4
A:184-222
B:184-222
C:184-222
D:184-222
39
39
39
39
1.8a
ENST00000286648
8a
ENSE00001076634
chr4:
71892382-71892472
91
DCK_HUMAN
222-252
31
4
A:222-252 (gaps)
B:222-252 (gaps)
C:222-252 (gaps)
D:222-252 (gaps)
31
31
31
31
1.10
ENST00000286648
10
ENSE00001235483
chr4:
71895069-71896631
1563
DCK_HUMAN
253-260
8
4
A:253-260
B:253-260
C:253-260
D:253-260
8
8
8
8
[
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2a30a_ (A:)
1b: SCOP_d2a30b_ (B:)
1c: SCOP_d2a30c_ (C:)
1d: SCOP_d2a30d_ (D:)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Nucleotide and nucleoside kinases
(231)
Protein domain
:
Deoxycytidine kinase
(35)
Human (Homo sapiens) [TaxId: 9606]
(35)
1a
d2a30a_
A:
1b
d2a30b_
B:
1c
d2a30c_
C:
1d
d2a30d_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2a30B00 (B:20-260)
1b: CATH_2a30D00 (D:20-260)
1c: CATH_2a30A00 (A:20-260)
1d: CATH_2a30C00 (C:20-260)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Human (Homo sapiens)
(413)
1a
2a30B00
B:20-260
1b
2a30D00
D:20-260
1c
2a30A00
A:20-260
1d
2a30C00
C:20-260
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Nucleic
Backbone
Sidechain
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Protein & NOT PROSITE
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Chain C
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (149 KB)
Header - Asym.Unit
Biol.Unit 1 (73 KB)
Header - Biol.Unit 1
Biol.Unit 2 (73 KB)
Header - Biol.Unit 2
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