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Asym. Unit
Info
Asym.Unit (173 KB)
Biol.Unit 1 (167 KB)
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(1)
Title
:
STRUCTURE OF NDPK H122G AND TENOFOVIR-DIPHOSPHATE
Authors
:
S. Morera, Y. X. Chen
Date
:
16 Dec 08 (Deposition) - 29 Sep 09 (Release) - 18 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
An Hexamer Structure, Atp-Binding, Kinase, Magnesium, Metal-Binding, Nucleotide Metabolism, Nucleotide-Binding, Phosphoprotein, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Koch, Y. X. Chen, J. Y. Feng, K. Borroto-Esoda, D. Deville-Bonne, S. Gallois-Montbrun, J. Janin, S. Morera
Nucleoside Diphosphate Kinase And The Activation Of Antiviral Phosphonate Analogs Of Nucleotides: Binding Mode And Phosphorylation Of Tenofovir Derivatives
Nucleosides Nucleotides V. 28 776 2009 Nucleic Acids
[
close entry info
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Hetero Components
(5, 19)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
4a: [(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-... (TNMa)
4b: [(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-... (TNMb)
4c: [(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-... (TNMc)
4d: [(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-... (TNMd)
4e: [(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-... (TNMe)
5a: [2-(6-AMINO-9H-PURIN-9-YL)-1-METHY... (TNVa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
2
Ligand/Ion
GLYCEROL
3
MG
6
Ligand/Ion
MAGNESIUM ION
4
TNM
5
Ligand/Ion
[(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-2-YL]OXYMETHYL-PHOSPHONOOXY-PHOSPHINIC ACID
5
TNV
1
Ligand/Ion
[2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE
[
close Hetero Component info
]
Sites
(19, 19)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:16 , PHE A:64 , LEU A:68 , ARG A:92 , THR A:98 , ARG A:109 , VAL A:116 , ASN A:119 , MG A:156 , HOH A:1016 , HOH A:1017 , HOH A:1019 , HOH A:1022 , HOH A:1282 , HOH A:1335 , HOH A:1428 , HOH A:1626 , HOH A:1627 , HOH A:1861 , HOH B:1863
BINDING SITE FOR RESIDUE TNM A 160
02
AC2
SOFTWARE
TNM A:160 , HOH A:1016 , HOH A:1019 , HOH A:1020 , HOH A:1335
BINDING SITE FOR RESIDUE MG A 156
03
AC3
SOFTWARE
GLU A:146 , LYS A:148 , HOH A:1928 , SER D:74 , GLY D:75 , PRO D:76
BINDING SITE FOR RESIDUE EDO A 157
04
AC4
SOFTWARE
LYS B:16 , HIS B:59 , PHE B:64 , LEU B:68 , ARG B:92 , THR B:98 , ARG B:109 , VAL B:116 , GLY B:117 , ASN B:119 , MG B:156 , HOH B:1011 , HOH B:1012 , HOH B:1554 , HOH B:1597 , HOH B:1814 , HOH B:1842 , HOH B:1843 , HOH B:1845 , HOH B:2040
BINDING SITE FOR RESIDUE TNM B 160
05
AC5
SOFTWARE
TNM B:160 , HOH B:1554 , HOH B:1597 , HOH B:1814 , HOH B:2040
BINDING SITE FOR RESIDUE MG B 156
06
AC6
SOFTWARE
VAL B:38 , LYS B:148 , HOH B:1405 , HOH B:1505 , HOH B:1694 , HOH B:1794 , ALA E:21 , HOH E:1641
BINDING SITE FOR RESIDUE EDO B 157
07
AC7
SOFTWARE
LYS C:16 , TYR C:56 , HIS C:59 , PHE C:64 , LEU C:68 , ARG C:92 , ARG C:109 , VAL C:116 , ASN C:119 , MG C:156 , HOH C:1013 , HOH C:1014 , HOH C:1317 , HOH C:1848 , HOH C:1849 , HOH C:1850 , HOH C:1851 , HOH C:2043 , HOH C:2158
BINDING SITE FOR RESIDUE TNM C 160
08
AC8
SOFTWARE
TNM C:160 , HOH C:1014 , HOH C:1849 , HOH C:1850 , HOH C:1851
BINDING SITE FOR RESIDUE MG C 156
09
AC9
SOFTWARE
ARG C:92 , GLY C:96 , VAL C:97 , THR C:98 , HOH C:1623 , HOH C:1856 , HOH C:1962
BINDING SITE FOR RESIDUE GOL C 157
10
BC1
SOFTWARE
LYS D:16 , TYR D:56 , GLU D:58 , HIS D:59 , PHE D:64 , ARG D:92 , ARG D:109 , VAL D:116 , GLY D:117 , ASN D:119 , MG D:156 , HOH D:1001 , HOH D:1005 , HOH D:1327 , HOH D:1831 , HOH D:1834 , HOH D:2154
BINDING SITE FOR RESIDUE TNV D 160
11
BC2
SOFTWARE
TNV D:160 , HOH D:1001 , HOH D:1831 , HOH D:1834
BINDING SITE FOR RESIDUE MG D 156
12
BC3
SOFTWARE
ASN D:99 , HOH D:2257 , HOH F:1599
BINDING SITE FOR RESIDUE GOL D 157
13
BC4
SOFTWARE
VAL D:38 , LYS D:148 , PRO D:149 , ASN D:150 , TYR D:154 , HOH D:1572 , HOH D:1961 , HOH D:2276
BINDING SITE FOR RESIDUE EDO D 158
14
BC5
SOFTWARE
HOH D:1868 , LYS E:16 , HIS E:59 , PHE E:64 , LEU E:68 , ARG E:92 , THR E:98 , ARG E:109 , VAL E:116 , ASN E:119 , MG E:156 , HOH E:1024 , HOH E:1025 , HOH E:1026 , HOH E:1028 , HOH E:1029 , HOH E:1032 , HOH E:1372 , HOH E:1581 , HOH E:1590 , HOH E:1864
BINDING SITE FOR RESIDUE TNM E 160
15
BC6
SOFTWARE
TNM E:160 , HOH E:1024 , HOH E:1025 , HOH E:1026 , HOH E:1029
BINDING SITE FOR RESIDUE MG E 156
16
BC7
SOFTWARE
GLU E:155 , HOH E:2090 , LYS F:16 , PHE F:64 , LEU F:68 , ARG F:92 , THR F:98 , ARG F:109 , VAL F:116 , ASN F:119 , MG F:156 , HOH F:1036 , HOH F:1038 , HOH F:1043 , HOH F:1045 , HOH F:1046 , HOH F:1049 , HOH F:1050 , HOH F:1106 , HOH F:1869
BINDING SITE FOR RESIDUE TNM F 160
17
BC8
SOFTWARE
TNM F:160 , HOH F:1043 , HOH F:1044 , HOH F:1045 , HOH F:1046
BINDING SITE FOR RESIDUE MG F 156
18
BC9
SOFTWARE
HOH E:1307 , GLY F:67 , SER F:70 , PHE F:71
BINDING SITE FOR RESIDUE EDO F 157
19
CC1
SOFTWARE
VAL F:6 , ASN F:7
BINDING SITE FOR RESIDUE EDO F 158
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: NDP_KINASES (A:119-127,B:119-127,C:119-127,D:11...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NDP_KINASES
PS00469
Nucleoside diphosphate kinases active site.
NDKC_DICDI
119-127
6
A:119-127
B:119-127
C:119-127
D:119-127
E:119-127
F:119-127
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 6)
Info
All SCOP Domains
1a: SCOP_d3fkba_ (A:)
1b: SCOP_d3fkbb_ (B:)
1c: SCOP_d3fkbc_ (C:)
1d: SCOP_d3fkbd_ (D:)
1e: SCOP_d3fkbe_ (E:)
1f: SCOP_d3fkbf_ (F:)
View:
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Classes
(
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)
Protein Domains
(
)
(
)
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
:
automated matches
(46)
Slime mold (Dictyostelium discoideum) [TaxId: 44689]
(3)
1a
d3fkba_
A:
1b
d3fkbb_
B:
1c
d3fkbc_
C:
1d
d3fkbd_
D:
1e
d3fkbe_
E:
1f
d3fkbf_
F:
[
close SCOP info
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
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