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2VP9
Biol. Unit 4
Info
Asym.Unit (273 KB)
Biol.Unit 1 (70 KB)
Biol.Unit 2 (70 KB)
Biol.Unit 3 (69 KB)
Biol.Unit 4 (69 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
:
27 Feb 08 (Deposition) - 29 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Atp-Binding, Dna Synthesis, Phosphoprotein, Feedback Inhibition, Deoxyribonucleoside Kinase, Salvage Pathway, Nucleotide-Binding, Dttp, Kinase, Complex, Drosophila, Transferase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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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
(2, 4)
Info
All Hetero Components
1a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
1b: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCb)
1c: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCc)
1d: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCd)
1e: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCe)
1f: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCf)
1g: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCg)
1h: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCh)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
View:
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Label:
No.
Name
Count
Type
Full Name
1
DOC
2
Mod. Residue
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
2
SO4
2
Ligand/Ion
SULFATE ION
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Sites
(5, 5)
Info
All Sites
1: AC6 (SOFTWARE)
2: AC8 (SOFTWARE)
3: AC9 (SOFTWARE)
4: BC6 (SOFTWARE)
5: BC7 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC6
SOFTWARE
GLY H:30 , SER H:31 , GLY H:32 , LYS H:33 , THR H:34 , ARG H:167
BINDING SITE FOR RESIDUE SO4 H1209
2
AC8
SOFTWARE
ASN G:28 , ILE G:29 , GLY G:30 , SER G:31 , GLY G:32 , LYS G:33 , THR G:34 , ARG G:167
BINDING SITE FOR RESIDUE SO4 G1209
3
AC9
SOFTWARE
ARG A:169 , ARG H:169
BINDING SITE FOR RESIDUE SO4 A1210
4
BC6
SOFTWARE
GLU G:52 , TRP G:57 , MET G:69 , TYR G:70 , PHE G:80 , GLN G:81 , VAL G:84 , ARG G:105 , ALA G:110 , PHE G:114
BINDING SITE FOR RESIDUE DOC G1210
5
BC7
SOFTWARE
ILE H:29 , GLU H:52 , MET H:69 , PHE H:80 , GLN H:81 , VAL H:84 , ARG H:105 , ALA H:110 , PHE H:114
BINDING SITE FOR RESIDUE DOC H1210
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d2vp9a_ (A:)
1b: SCOP_d2vp9b_ (B:)
1c: SCOP_d2vp9c_ (C:)
1d: SCOP_d2vp9d_ (D:)
1e: SCOP_d2vp9e_ (E:)
1f: SCOP_d2vp9f_ (F:)
1g: SCOP_d2vp9g_ (G:)
1h: SCOP_d2vp9h_ (H:)
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Protein Domains
(
)
(
)
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
:
Deoxyribonucleoside kinase
(11)
Fruit fly (Drosophila melanogaster) [TaxId: 7227]
(11)
1a
d2vp9a_
A:
1b
d2vp9b_
B:
1c
d2vp9c_
C:
1d
d2vp9d_
D:
1e
d2vp9e_
E:
1f
d2vp9f_
F:
1g
d2vp9g_
G:
1h
d2vp9h_
H:
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2vp9A00 (A:12-208)
1b: CATH_2vp9C00 (C:12-208)
1c: CATH_2vp9B00 (B:12-208)
1d: CATH_2vp9E00 (E:12-208)
1e: CATH_2vp9F00 (F:12-208)
1f: CATH_2vp9G00 (G:12-208)
1g: CATH_2vp9H00 (H:12-208)
1h: CATH_2vp9D00 (D: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
2vp9A00
A:12-208
1b
2vp9C00
C:12-208
1c
2vp9B00
B:12-208
1d
2vp9E00
E:12-208
1e
2vp9F00
F:12-208
1f
2vp9G00
G:12-208
1g
2vp9H00
H:12-208
1h
2vp9D00
D:12-208
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_dNK_2vp9H01 (H:80-208)
1b: PFAM_dNK_2vp9H02 (H:80-208)
1c: PFAM_dNK_2vp9H03 (H:80-208)
1d: PFAM_dNK_2vp9H04 (H:80-208)
1e: PFAM_dNK_2vp9H05 (H:80-208)
1f: PFAM_dNK_2vp9H06 (H:80-208)
1g: PFAM_dNK_2vp9H07 (H:80-208)
1h: PFAM_dNK_2vp9H08 (H:80-208)
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Clan
:
P-loop_NTPase
(1112)
Family
:
dNK
(33)
Drosophila melanogaster (Fruit fly)
(13)
1a
dNK-2vp9H01
H:80-208
1b
dNK-2vp9H02
H:80-208
1c
dNK-2vp9H03
H:80-208
1d
dNK-2vp9H04
H:80-208
1e
dNK-2vp9H05
H:80-208
1f
dNK-2vp9H06
H:80-208
1g
dNK-2vp9H07
H:80-208
1h
dNK-2vp9H08
H:80-208
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Asymmetric Unit 1
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Asym.Unit (273 KB)
Header - Asym.Unit
Biol.Unit 1 (70 KB)
Header - Biol.Unit 1
Biol.Unit 2 (70 KB)
Header - Biol.Unit 2
Biol.Unit 3 (69 KB)
Header - Biol.Unit 3
Biol.Unit 4 (69 KB)
Header - Biol.Unit 4
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