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1S57
Biol. Unit 1
Info
Asym.Unit (163 KB)
Biol.Unit 1 (157 KB)
Biol.Unit 2 (158 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE 2 FROM ARABIDOPSIS
Authors
:
Y. J. Im, J. -I. Kim, Y. Shen, Y. Na, Y. -J. Han, S. -H. Kim, P. -S. Song, S. H. Eom
Date
:
20 Jan 04 (Deposition) - 30 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: A,B,C,D,E,F (1x)
Keywords
:
Transferase, Kinase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. J. Im, J. -I. Kim, Y. Shen, Y. Na, Y. -J. Han, S. -H. Kim, P. -S. Song, S. H. Eom
Structural Analysis Of Arabidopsis Thaliana Nucleoside Diphosphate Kinase-2 For Phytochrome-Mediated Light Signaling
J. Mol. Biol. V. 343 659 2004
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(2, 24)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
1c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
1d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
1e: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEe)
1f: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEf)
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)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
6
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
SO4
18
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:167
BINDING SITE FOR RESIDUE SO4 A 1001
02
AC2
SOFTWARE
ARG A:167 , THR A:173 , ARG A:184 , HIS A:197 , HOH A:1137 , HOH A:1176
BINDING SITE FOR RESIDUE SO4 A 1002
03
AC3
SOFTWARE
LYS A:172 , THR A:173 , HOH A:1114 , HOH A:1164
BINDING SITE FOR RESIDUE SO4 A 1003
04
AC4
SOFTWARE
ARG B:167 , HOH B:1179 , LYS D:206
BINDING SITE FOR RESIDUE SO4 B 1004
05
AC5
SOFTWARE
LYS B:91 , ARG B:167 , THR B:173 , ARG B:184 , HIS B:197 , HOH B:1134
BINDING SITE FOR RESIDUE SO4 B 1005
06
AC6
SOFTWARE
LYS B:172 , THR B:173 , HOH B:1178 , HOH B:1179 , ASP D:82 , LYS D:206 , HOH D:1193
BINDING SITE FOR RESIDUE SO4 B 1006
07
AC7
SOFTWARE
ARG C:167 , HOH C:1156 , HOH C:1161
BINDING SITE FOR RESIDUE SO4 C 1007
08
AC8
SOFTWARE
LYS C:91 , ARG C:184 , HIS C:197
BINDING SITE FOR RESIDUE SO4 C 1008
09
AC9
SOFTWARE
LYS C:172 , THR C:173 , HOH C:1128
BINDING SITE FOR RESIDUE SO4 C 1009
10
BC1
SOFTWARE
ARG D:167 , HOH D:1185 , HOH D:1189
BINDING SITE FOR RESIDUE SO4 D 1010
11
BC2
SOFTWARE
LYS D:91 , ARG D:167 , ARG D:184 , HIS D:197 , HOH D:1134 , HOH D:1188 , HOH D:1212
BINDING SITE FOR RESIDUE SO4 D 1011
12
BC3
SOFTWARE
LYS D:172 , THR D:173 , HOH D:1108
BINDING SITE FOR RESIDUE SO4 D 1012
13
BC4
SOFTWARE
ARG E:167 , HOH E:1061 , HOH E:1082
BINDING SITE FOR RESIDUE SO4 E 1013
14
BC5
SOFTWARE
ARG E:167 , THR E:173 , ARG E:184 , HOH E:1062 , HOH E:1076
BINDING SITE FOR RESIDUE SO4 E 1014
15
BC6
SOFTWARE
LYS E:172 , THR E:173 , HOH E:1028 , HOH E:1058 , HOH E:1074
BINDING SITE FOR RESIDUE SO4 E 1015
16
BC7
SOFTWARE
ARG F:167 , HOH F:1162
BINDING SITE FOR RESIDUE SO4 F 1016
17
BC8
SOFTWARE
ARG F:167 , ARG F:184 , HIS F:197 , HOH F:1159 , HOH F:1179
BINDING SITE FOR RESIDUE SO4 F 1017
18
BC9
SOFTWARE
LYS F:172 , THR F:173 , HOH F:1117
BINDING SITE FOR RESIDUE SO4 F 1018
19
CC1
SOFTWARE
GLU A:108 , GLY A:111 , PHE A:112 , LYS A:113 , TRP A:221 , SER A:223 , ALA A:226 , ARG A:230 , HOH A:1106 , HOH A:1110 , HOH A:1111 , HOH A:1152 , GLN D:96 , ARG D:97 , GLY D:98
BINDING SITE FOR RESIDUE EPE A 1101
20
CC2
SOFTWARE
GLU B:108 , GLY B:111 , TRP B:221 , SER B:223 , ALA B:226 , ARG B:230 , HOH B:1133 , HOH B:1138 , HOH B:1143 , HOH B:1147 , HOH B:1165 , HOH B:1170 , GLN F:96 , ARG F:97 , GLY F:98
BINDING SITE FOR RESIDUE EPE B 1102
21
CC3
SOFTWARE
GLU C:108 , GLY C:111 , PHE C:112 , LYS C:113 , TRP C:221 , SER C:223 , LEU C:229 , ARG C:230 , HOH C:1110 , HOH C:1131 , HOH C:1134 , HOH C:1142 , HOH C:1148 , HOH C:1164 , GLN E:96 , ARG E:97 , GLY E:98
BINDING SITE FOR RESIDUE EPE C 1103
22
CC4
SOFTWARE
GLN A:96 , ARG A:97 , GLY A:98 , GLU D:108 , GLY D:111 , PHE D:112 , LYS D:113 , TRP D:221 , SER D:223 , ALA D:226 , LEU D:229 , ARG D:230 , HOH D:1114 , HOH D:1115 , HOH D:1128 , HOH D:1200 , HOH D:1204 , HOH E:1035
BINDING SITE FOR RESIDUE EPE D 1104
23
CC5
SOFTWARE
GLN C:96 , ARG C:97 , GLY C:98 , HOH C:1127 , HOH C:1132 , HOH C:1160 , GLU E:108 , GLY E:111 , PHE E:112 , TRP E:221 , SER E:223 , ALA E:226 , HOH E:1067 , HOH E:1085
BINDING SITE FOR RESIDUE EPE C 1105
24
CC6
SOFTWARE
GLN B:96 , ARG B:97 , GLY B:98 , GLU F:108 , GLY F:111 , PHE F:112 , TRP F:221 , SER F:223 , LEU F:229 , HOH F:1114 , HOH F:1116 , HOH F:1142 , HOH F:1184
BINDING SITE FOR RESIDUE EPE F 1106
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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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:194-202,B:194-202,C:194-202,D:19...)
;
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.
NDK2_ARATH
194-202
6
A:194-202
B:194-202
C:194-202
D:194-202
E:194-202
F:194-202
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1s57a_ (A:)
1b: SCOP_d1s57b_ (B:)
1c: SCOP_d1s57c_ (C:)
1d: SCOP_d1s57d_ (D:)
1e: SCOP_d1s57e_ (E:)
1f: SCOP_d1s57f_ (F:)
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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
:
Nucleoside diphosphate kinase, NDK
(66)
Thale cress (Arabidopsis thaliana), chloroplast NDK2 [TaxId: 3702]
(2)
1a
d1s57a_
A:
1b
d1s57b_
B:
1c
d1s57c_
C:
1d
d1s57d_
D:
1e
d1s57e_
E:
1f
d1s57f_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1s57B00 (B:83-231)
1b: CATH_1s57C00 (C:83-231)
1c: CATH_1s57E00 (E:83-231)
1d: CATH_1s57A00 (A:79-231)
1e: CATH_1s57D00 (D:79-231)
1f: CATH_1s57F00 (F:79-231)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.141, no name defined]
(46)
Thale cress (Arabidopsis thaliana)
(3)
1a
1s57B00
B:83-231
1b
1s57C00
C:83-231
1c
1s57E00
E:83-231
1d
1s57A00
A:79-231
1e
1s57D00
D:79-231
1f
1s57F00
F:79-231
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_NDK_1s57F01 (F:84-218)
1b: PFAM_NDK_1s57F02 (F:84-218)
1c: PFAM_NDK_1s57F03 (F:84-218)
1d: PFAM_NDK_1s57F04 (F:84-218)
1e: PFAM_NDK_1s57F05 (F:84-218)
1f: PFAM_NDK_1s57F06 (F:84-218)
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Clans
(
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(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NDK]
(40)
Family
:
NDK
(40)
Arabidopsis thaliana (Mouse-ear cress)
(3)
1a
NDK-1s57F01
F:84-218
1b
NDK-1s57F02
F:84-218
1c
NDK-1s57F03
F:84-218
1d
NDK-1s57F04
F:84-218
1e
NDK-1s57F05
F:84-218
1f
NDK-1s57F06
F:84-218
[
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]
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (163 KB)
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