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2VP4
Asym. Unit
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Asym.Unit (150 KB)
Biol.Unit 1 (144 KB)
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(1)
Title
:
STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE
Authors
:
N. E. Mikkelsen, B. Munch-Petersen, H. Eklund
Date
:
26 Feb 08 (Deposition) - 29 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Atp-Binding, Dna Synthesis, Phosphoprotein, Feedback Inhibition, Deoxyribonucleoside Kinase, Salvage Pathway, Nucleotide-Binding, Dttp, Kinase, Complex, Drosophila, Transferase
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Reference
:
N. E. Mikkelsen, B. Munch-Petersen, H. Eklund
Structural Studies Of Nucleoside Analog And Feedback Inhibitor Binding To Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase.
Febs J. V. 275 2151 2008
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPa)
1b: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPb)
1c: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPc)
1d: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPd)
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No.
Name
Count
Type
Full Name
1
DCP
4
Ligand/Ion
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE D:29 , GLY D:30 , SER D:31 , GLY D:32 , LYS D:33 , THR D:34 , TRP D:57 , LEU D:66 , MET D:69 , TYR D:70 , PHE D:80 , GLN D:81 , VAL D:84 , GLU D:104 , ARG D:105 , ALA D:110 , PHE D:114 , MET D:118 , ARG D:167 , ARG D:169 , GLU D:172 , HOH D:2085 , HOH D:2103 , HOH D:2104 , HOH D:2105
BINDING SITE FOR RESIDUE DCP D1211
2
AC2
SOFTWARE
ILE C:29 , GLY C:30 , SER C:31 , GLY C:32 , LYS C:33 , THR C:34 , TRP C:57 , LEU C:66 , MET C:69 , TYR C:70 , PHE C:80 , GLN C:81 , VAL C:84 , GLU C:104 , ARG C:105 , ALA C:110 , PHE C:114 , MET C:118 , ARG C:167 , ARG C:169 , GLU C:172 , HOH C:2089 , HOH C:2104 , HOH C:2105 , HOH C:2106
BINDING SITE FOR RESIDUE DCP C1209
3
AC3
SOFTWARE
ILE B:29 , GLY B:30 , SER B:31 , GLY B:32 , LYS B:33 , THR B:34 , VAL B:54 , TRP B:57 , TYR B:70 , PHE B:80 , GLN B:81 , VAL B:84 , GLU B:104 , ARG B:105 , ALA B:110 , PHE B:114 , ARG B:167 , ARG B:169 , GLU B:172 , HOH B:2099 , HOH B:2119 , HOH B:2120 , HOH B:2121
BINDING SITE FOR RESIDUE DCP B1210
4
AC4
SOFTWARE
ILE A:29 , GLY A:30 , SER A:31 , GLY A:32 , LYS A:33 , THR A:34 , TRP A:57 , LEU A:66 , MET A:69 , TYR A:70 , PHE A:80 , GLN A:81 , VAL A:84 , GLU A:104 , ARG A:105 , ALA A:110 , PHE A:114 , ARG A:167 , ARG A:169 , GLU A:172 , HOH A:2105 , HOH A:2125 , HOH A:2126 , HOH A:2127
BINDING SITE FOR RESIDUE DCP A1210
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SAPs(SNPs)/Variants
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Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2vp4a_ (A:)
1b: SCOP_d2vp4b_ (B:)
1c: SCOP_d2vp4c_ (C:)
1d: SCOP_d2vp4d_ (D:)
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Protein Domains
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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
:
Deoxyribonucleoside kinase
(11)
Fruit fly (Drosophila melanogaster) [TaxId: 7227]
(11)
1a
d2vp4a_
A:
1b
d2vp4b_
B:
1c
d2vp4c_
C:
1d
d2vp4d_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2vp4D00 (D:12-210)
1b: CATH_2vp4A00 (A:12-209)
1c: CATH_2vp4B00 (B:12-209)
1d: CATH_2vp4C00 (C:12-208)
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Organisms
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Fruit fly (Drosophila melanogaster)
(15)
1a
2vp4D00
D:12-210
1b
2vp4A00
A:12-209
1c
2vp4B00
B:12-209
1d
2vp4C00
C:12-208
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_dNK_2vp4D01 (D:80-210)
1b: PFAM_dNK_2vp4D02 (D:80-210)
1c: PFAM_dNK_2vp4D03 (D:80-210)
1d: PFAM_dNK_2vp4D04 (D:80-210)
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Clan
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P-loop_NTPase
(1112)
Family
:
dNK
(33)
Drosophila melanogaster (Fruit fly)
(13)
1a
dNK-2vp4D01
D:80-210
1b
dNK-2vp4D02
D:80-210
1c
dNK-2vp4D03
D:80-210
1d
dNK-2vp4D04
D:80-210
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Asymmetric Unit 1
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