Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1S57

crystal structure of nucleoside diphosphate kinase 2 from Arabidopsis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0006183	biological_process	GTP biosynthetic process
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0006183	biological_process	GTP biosynthetic process
E	0006228	biological_process	UTP biosynthetic process
E	0006241	biological_process	CTP biosynthetic process
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0006183	biological_process	GTP biosynthetic process
F	0006228	biological_process	UTP biosynthetic process
F	0006241	biological_process	CTP biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SO4 A 1001

Chain	Residue
A	ARG167

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 1002

Chain	Residue
A	ARG167
A	THR173
A	ARG184
A	HIS197
A	HOH1137
A	HOH1176

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 1003

Chain	Residue
A	HOH1114
A	HOH1164
A	LYS172
A	THR173

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 1004

Chain	Residue
B	ARG167
B	HOH1179
D	LYS206

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 1005

Chain	Residue
B	LYS91
B	ARG167
B	THR173
B	ARG184
B	HIS197
B	HOH1134

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 1006

Chain	Residue
B	LYS172
B	THR173
B	HOH1178
B	HOH1179
D	ASP82
D	LYS206
D	HOH1193

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 1007

Chain	Residue
C	ARG167
C	HOH1156
C	HOH1161

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 1008

Chain	Residue
C	LYS91
C	ARG184
C	HIS197

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 1009

Chain	Residue
C	LYS172
C	THR173
C	HOH1128

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 1010

Chain	Residue
D	ARG167
D	HOH1185
D	HOH1189

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 D 1011

Chain	Residue
D	LYS91
D	ARG167
D	ARG184
D	HIS197
D	HOH1134
D	HOH1188
D	HOH1212

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 1012

Chain	Residue
D	LYS172
D	THR173
D	HOH1108

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 1013

Chain	Residue
E	ARG167
E	HOH1061
E	HOH1082

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 1014

Chain	Residue
E	ARG167
E	THR173
E	ARG184
E	HOH1062
E	HOH1076

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 1015

Chain	Residue
E	LYS172
E	THR173
E	HOH1028
E	HOH1058
E	HOH1074

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 F 1016

Chain	Residue
F	ARG167
F	HOH1162

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 F 1017

Chain	Residue
F	ARG167
F	ARG184
F	HIS197
F	HOH1159
F	HOH1179

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 F 1018

Chain	Residue
F	LYS172
F	THR173
F	HOH1117

site_id	CC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE EPE A 1101

Chain	Residue
A	GLU108
A	GLY111
A	PHE112
A	LYS113
A	TRP221
A	SER223
A	ALA226
A	ARG230
A	HOH1106
A	HOH1110
A	HOH1111
A	HOH1152
D	GLN96
D	ARG97
D	GLY98

site_id	CC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE EPE B 1102

Chain	Residue
F	GLN96
F	ARG97
F	GLY98
B	GLU108
B	GLY111
B	TRP221
B	SER223
B	ALA226
B	ARG230
B	HOH1133
B	HOH1138
B	HOH1143
B	HOH1147
B	HOH1165
B	HOH1170

site_id	CC3
Number of Residues	17
Details	BINDING SITE FOR RESIDUE EPE C 1103

Chain	Residue
C	GLU108
C	GLY111
C	PHE112
C	LYS113
C	TRP221
C	SER223
C	LEU229
C	ARG230
C	HOH1110
C	HOH1131
C	HOH1134
C	HOH1142
C	HOH1148
C	HOH1164
E	GLN96
E	ARG97
E	GLY98

site_id	CC4
Number of Residues	18
Details	BINDING SITE FOR RESIDUE EPE D 1104

Chain	Residue
A	GLN96
A	ARG97
A	GLY98
D	GLU108
D	GLY111
D	PHE112
D	LYS113
D	TRP221
D	SER223
D	ALA226
D	LEU229
D	ARG230
D	HOH1114
D	HOH1115
D	HOH1128
D	HOH1200
D	HOH1204
E	HOH1035

site_id	CC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE EPE C 1105

Chain	Residue
C	GLN96
C	ARG97
C	GLY98
C	HOH1127
C	HOH1132
C	HOH1160
E	GLU108
E	GLY111
E	PHE112
E	TRP221
E	SER223
E	ALA226
E	HOH1067
E	HOH1085

site_id	CC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE EPE F 1106

Chain	Residue
B	GLN96
B	ARG97
B	GLY98
F	GLU108
F	GLY111
F	PHE112
F	TRP221
F	SER223
F	LEU229
F	HOH1114
F	HOH1116
F	HOH1142
F	HOH1184

Functional Information from PROSITE/UniProt

site_id	PS00469
Number of Residues	9
Details	NDPK Nucleoside diphosphate kinase (NDPK) active site signature. NivHGSDSP

Chain	Residue	Details
A	ASN194-PRO202

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	36
Details	Binding site: {}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
A	LYS91
A	ASN194

site_id	CSA10
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
D	TYR131
D	LYS91

site_id	CSA11
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
E	TYR131
E	LYS91

site_id	CSA12
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
F	TYR131
F	LYS91

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
B	LYS91
B	ASN194

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
C	LYS91
C	ASN194

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
D	LYS91
D	ASN194

site_id	CSA5
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
E	LYS91
E	ASN194

site_id	CSA6
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
F	LYS91
F	ASN194

site_id	CSA7
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
A	TYR131
A	LYS91

site_id	CSA8
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
B	TYR131
B	LYS91

site_id	CSA9
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
C	TYR131
C	LYS91

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)