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2PLR
Asym. Unit
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Asym.Unit (91 KB)
Biol.Unit 1 (85 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DTMP KINASE (ST1543) FROM SULFOLOBUS TOKODAII STRAIN7
Authors
:
S. P. Kanaujia, J. Jeyakanthan, Z. A. Rafi, K. Sekar, N. Nakagawa, A. Ebi S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
20 Apr 07 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Tmp-Binding, Atp-Binding, Thymidylate Kinase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. P. Kanaujia, J. Jeyakanthan, Z. A. Rafi, K. Sekar, N. Nakagawa, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of Dtmp Kinase (St1543) From Sulfolobus Tokodaii Strain7
To Be Published
[
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Hetero Components
(10, 31)
Info
All Hetero Components
01a: PENTAETHYLENE GLYCOL (1PEa)
01b: PENTAETHYLENE GLYCOL (1PEb)
01c: PENTAETHYLENE GLYCOL (1PEc)
02a: CHLORIDE ION (CLa)
02b: CHLORIDE ION (CLb)
03a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
04a: 1,2-ETHANEDIOL (EDOa)
04b: 1,2-ETHANEDIOL (EDOb)
04c: 1,2-ETHANEDIOL (EDOc)
04d: 1,2-ETHANEDIOL (EDOd)
04e: 1,2-ETHANEDIOL (EDOe)
04f: 1,2-ETHANEDIOL (EDOf)
05a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
06a: SELENOMETHIONINE (MSEa)
06b: SELENOMETHIONINE (MSEb)
07a: DI(HYDROXYETHYL)ETHER (PEGa)
07b: DI(HYDROXYETHYL)ETHER (PEGb)
07c: DI(HYDROXYETHYL)ETHER (PEGc)
07d: DI(HYDROXYETHYL)ETHER (PEGd)
07e: DI(HYDROXYETHYL)ETHER (PEGe)
07f: DI(HYDROXYETHYL)ETHER (PEGf)
07g: DI(HYDROXYETHYL)ETHER (PEGg)
07h: DI(HYDROXYETHYL)ETHER (PEGh)
07i: DI(HYDROXYETHYL)ETHER (PEGi)
07j: DI(HYDROXYETHYL)ETHER (PEGj)
07k: DI(HYDROXYETHYL)ETHER (PEGk)
08a: TETRAETHYLENE GLYCOL (PG4a)
09a: TRIETHYLENE GLYCOL (PGEa)
09b: TRIETHYLENE GLYCOL (PGEb)
09c: TRIETHYLENE GLYCOL (PGEc)
10a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
3
Ligand/Ion
PENTAETHYLENE GLYCOL
2
CL
2
Ligand/Ion
CHLORIDE ION
3
DTT
1
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
4
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
5
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6
MSE
2
Mod. Amino Acid
SELENOMETHIONINE
7
PEG
11
Ligand/Ion
DI(HYDROXYETHYL)ETHER
8
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
9
PGE
3
Ligand/Ion
TRIETHYLENE GLYCOL
10
PO4
1
Ligand/Ion
PHOSPHATE ION
[
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Sites
(27, 27)
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)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:13 , ARG A:93 , GLN A:169
BINDING SITE FOR RESIDUE CL A 214
02
AC2
SOFTWARE
ARG A:101 , TYR A:168 , HOH A:2112 , HOH A:2185
BINDING SITE FOR RESIDUE CL A 215
03
AC3
SOFTWARE
ASP A:13 , GLY A:14 , SER A:15 , GLY A:16 , LYS A:17 , SER A:18 , HOH A:2049 , HOH A:2094 , HOH A:2097
BINDING SITE FOR RESIDUE PO4 A 1901
04
AC4
SOFTWARE
LYS A:113 , ASP A:182 , HOH A:2003 , ILE B:109 , LEU B:159 , LYS B:178 , HOH B:1619 , HOH B:1633
BINDING SITE FOR RESIDUE 1PE B 1301
05
AC5
SOFTWARE
LYS A:114 , SER A:117 , HOH A:2006 , HOH A:2023 , TRP B:111 , LYS B:114 , GLU B:174 , HOH B:1649
BINDING SITE FOR RESIDUE 1PE A 1302
06
AC6
SOFTWARE
ASP B:110 , LYS B:114 , ILE B:155 , PHE B:156
BINDING SITE FOR RESIDUE 1PE B 1303
07
AC7
SOFTWARE
SER A:103 , GLU A:174 , LYS A:178 , GLY B:158 , LEU B:159
BINDING SITE FOR RESIDUE PGE A 1401
08
AC8
SOFTWARE
ASP A:177 , HOH A:2138 , PRO B:157
BINDING SITE FOR RESIDUE PGE A 1402
09
AC9
SOFTWARE
LYS A:140 , LYS A:203 , PHE A:204 , GLU A:207 , HOH A:2200
BINDING SITE FOR RESIDUE PGE A 1404
10
BC1
SOFTWARE
GLU A:29 , LYS A:31 , ARG A:32
BINDING SITE FOR RESIDUE EDO A 1501
11
BC2
SOFTWARE
SER B:117 , ALA B:119
BINDING SITE FOR RESIDUE EDO B 1502
12
BC3
SOFTWARE
LYS B:55 , HOH B:1626
BINDING SITE FOR RESIDUE EDO B 1503
13
BC4
SOFTWARE
ARG A:77 , HOH A:2017
BINDING SITE FOR RESIDUE EDO A 1504
14
BC5
SOFTWARE
TRP A:27 , LYS A:31 , ASP A:47 , HOH A:2197
BINDING SITE FOR RESIDUE EDO A 1505
15
BC6
SOFTWARE
LYS A:121 , GLU A:183 , HOH A:1982 , ARG B:129 , ASP B:177 , HOH B:1719 , HOH B:1806
BINDING SITE FOR RESIDUE PG4 B 1601
16
BC7
SOFTWARE
PRO A:60 , PHE A:63 , HIS A:67 , ASP A:102 , ARG A:105 , ASP A:154 , HOH A:2134
BINDING SITE FOR RESIDUE DTT A 1701
17
BC8
SOFTWARE
TYR A:35 , THR A:37 , SER A:41 , SER A:42 , ASP A:43 , ARG A:74 , TYR A:78 , HOH A:2179
BINDING SITE FOR RESIDUE EPE A 1801
18
BC9
SOFTWARE
TRP A:39 , HIS A:67 , ASP A:70 , ARG A:74 , HOH A:2037 , HOH A:2041
BINDING SITE FOR RESIDUE PEG A 1201
19
CC1
SOFTWARE
ASP A:108 , TRP A:111 , HOH A:2000 , HOH A:2180 , PHE B:118
BINDING SITE FOR RESIDUE PEG A 1202
20
CC2
SOFTWARE
SER A:117 , ASP B:108 , TRP B:111 , HOH B:1728 , HOH B:1733
BINDING SITE FOR RESIDUE PEG B 1203
21
CC3
SOFTWARE
GLY A:14 , ARG A:138
BINDING SITE FOR RESIDUE PEG A 1204
22
CC4
SOFTWARE
ARG A:129 , ASP A:177 , HOH A:1913
BINDING SITE FOR RESIDUE PEG A 1206
23
CC5
SOFTWARE
HOH A:2131 , HOH A:2196 , HOH A:2206
BINDING SITE FOR RESIDUE PEG A 1207
24
CC6
SOFTWARE
ASN A:184 , ILE A:186 , HOH A:2034 , LYS B:181 , HOH B:1709 , HOH B:1800
BINDING SITE FOR RESIDUE PEG A 1208
25
CC7
SOFTWARE
ARG A:129 , SER A:131 , PRO A:132 , THR A:173 , LYS B:53 , LYS B:54 , ASP B:56
BINDING SITE FOR RESIDUE PEG B 1209
26
CC8
SOFTWARE
LEU B:58 , ASP B:154
BINDING SITE FOR RESIDUE PEG B 1210
27
CC9
SOFTWARE
HOH A:2021 , LEU B:136 , LYS B:140 , GLU B:162 , GLU B:163 , LEU B:166
BINDING SITE FOR RESIDUE PEG B 1211
[
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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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All 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
(0, 0)
Info
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Thymidylate_kin_2plrB01 (B:9-201)
1b: PFAM_Thymidylate_kin_2plrB02 (B:9-201)
View:
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Clans
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Families
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(
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Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Thymidylate_kin
(26)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
(1)
1a
Thymidylate_kin-2plrB01
B:9-201
1b
Thymidylate_kin-2plrB02
B:9-201
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