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3MJR
Asym. Unit
Info
Asym.Unit (155 KB)
Biol.Unit 1 (78 KB)
Biol.Unit 2 (73 KB)
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(1)
Title
:
HUMAN DCK COMPLEX WITH ACYCLIC NUCLEOSIDE
Authors
:
S. Hazra, A. Lavie
Date
:
13 Apr 10 (Deposition) - 28 Jul 10 (Release) - 18 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Acv, Gcv, Dck, Kinase, Udp, P-Loop, Kinase Activity, Nucleoside Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Hazra, M. Konrad, A. Lavie
The Sugar Ring Of The Nucleoside Is Required For Productive Substrate Positioning In The Active Site Of Human Deoxycytidine Kinase (Dck): Implications For The Developmen Of Dck-Activated Acyclic Guanine Analogues.
J. Med. Chem. V. 53 5792 2010
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: 9-HYROXYETHOXYMETHYLGUANINE (AC2a)
1b: 9-HYROXYETHOXYMETHYLGUANINE (AC2b)
1c: 9-HYROXYETHOXYMETHYLGUANINE (AC2c)
2a: URIDINE-5'-DIPHOSPHATE (UDPa)
2b: URIDINE-5'-DIPHOSPHATE (UDPb)
2c: URIDINE-5'-DIPHOSPHATE (UDPc)
2d: URIDINE-5'-DIPHOSPHATE (UDPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AC2
3
Ligand/Ion
9-HYROXYETHOXYMETHYLGUANINE
2
UDP
4
Ligand/Ion
URIDINE-5'-DIPHOSPHATE
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:30 , GLU A:53 , PHE A:96 , GLN A:97 , ARG A:128 , ASP A:133 , PHE A:137 , TYR A:204
BINDING SITE FOR RESIDUE AC2 A 301
2
AC2
SOFTWARE
ALA A:31 , ALA A:32 , GLY A:33 , LYS A:34 , SER A:35 , THR A:36 , GLU A:127 , ARG A:188 , ARG A:192 , ASP A:241 , PHE A:242 , LYS A:243
BINDING SITE FOR RESIDUE UDP A 261
3
AC3
SOFTWARE
GLU B:53 , VAL B:55 , PHE B:96 , GLN B:97 , ARG B:104 , ARG B:128 , ASP B:133 , PHE B:137 , HOH B:275
BINDING SITE FOR RESIDUE AC2 B 401
4
AC4
SOFTWARE
ALA B:31 , ALA B:32 , GLY B:33 , LYS B:34 , SER B:35 , THR B:36 , ARG B:188 , LEU B:191 , ARG B:192 , ASP B:241 , PHE B:242
BINDING SITE FOR RESIDUE UDP B 261
5
AC5
SOFTWARE
ALA C:31 , GLY C:33 , LYS C:34 , SER C:35 , THR C:36 , GLU C:127 , ARG C:188 , LEU C:191 , ARG C:192 , ASP C:241 , PHE C:242 , LYS C:243
BINDING SITE FOR RESIDUE UDP C 501
6
AC6
SOFTWARE
GLU D:53 , TYR D:86 , GLN D:97 , ARG D:104 , ARG D:128 , ASP D:133 , PHE D:137
BINDING SITE FOR RESIDUE AC2 D 601
7
AC7
SOFTWARE
ALA D:31 , ALA D:32 , GLY D:33 , LYS D:34 , SER D:35 , THR D:36 , ARG D:188 , LEU D:191 , ARG D:192 , ASP D:241 , PHE D:242
BINDING SITE FOR RESIDUE UDP D 261
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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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:31-60 | B:31-60 | C:31-59 | D:31...)
Exon 1.5 (A:71-134 | B:75-134 | C:74-134 (ga...)
Exon 1.6 (A:134-183 (gaps) | B:134-183 (gaps...)
Exon 1.7a (A:184-222 | B:184-222 | C:184-222 ...)
Exon 1.8a (A:222-252 | B:222-252 | C:222-252 ...)
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:
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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
1.3a
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:31-60
B:31-60
C:31-59
D:31-58 (gaps)
30
30
29
28
1.5
ENST00000286648
5
ENSE00001024734
chr4:
71888084-71888277
194
DCK_HUMAN
70-134
65
4
A:71-134
B:75-134
C:74-134 (gaps)
D:77-134
64
60
61
58
1.6
ENST00000286648
6
ENSE00001024731
chr4:
71889276-71889423
148
DCK_HUMAN
134-183
50
4
A:134-183 (gaps)
B:134-183 (gaps)
C:134-183 (gaps)
D:134-183 (gaps)
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
B:222-252
C:222-252
D:222-252
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_d3mjra_ (A:)
1b: SCOP_d3mjrb_ (B:)
1c: SCOP_d3mjrc_ (C:)
1d: SCOP_d3mjrd_ (D:)
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Organisms
(
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(
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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
d3mjra_
A:
1b
d3mjrb_
B:
1c
d3mjrc_
C:
1d
d3mjrd_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_dNK_3mjrD01 (D:96-253)
1b: PFAM_dNK_3mjrD02 (D:96-253)
1c: PFAM_dNK_3mjrD03 (D:96-253)
1d: PFAM_dNK_3mjrD04 (D:96-253)
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Clan
:
P-loop_NTPase
(1112)
Family
:
dNK
(33)
Homo sapiens (Human)
(20)
1a
dNK-3mjrD01
D:96-253
1b
dNK-3mjrD02
D:96-253
1c
dNK-3mjrD03
D:96-253
1d
dNK-3mjrD04
D:96-253
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Chain D
Asymmetric Unit 1
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Asym.Unit (155 KB)
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