Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1PKU

Crystal Structure of Nucleoside Diphosphate Kinase from Rice

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0005524	molecular_function	ATP binding
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0009117	biological_process	nucleotide metabolic process
A	0016301	molecular_function	kinase activity
A	0046872	molecular_function	metal ion binding
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0005524	molecular_function	ATP binding
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0009117	biological_process	nucleotide metabolic process
B	0016301	molecular_function	kinase activity
B	0046872	molecular_function	metal ion binding
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0005524	molecular_function	ATP binding
C	0006183	biological_process	GTP biosynthetic process
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
C	0009117	biological_process	nucleotide metabolic process
C	0016301	molecular_function	kinase activity
C	0046872	molecular_function	metal ion binding
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0005524	molecular_function	ATP binding
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
D	0009117	biological_process	nucleotide metabolic process
D	0016301	molecular_function	kinase activity
D	0046872	molecular_function	metal ion binding
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0005524	molecular_function	ATP binding
E	0006183	biological_process	GTP biosynthetic process
E	0006228	biological_process	UTP biosynthetic process
E	0006241	biological_process	CTP biosynthetic process
E	0009117	biological_process	nucleotide metabolic process
E	0016301	molecular_function	kinase activity
E	0046872	molecular_function	metal ion binding
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0005524	molecular_function	ATP binding
F	0006183	biological_process	GTP biosynthetic process
F	0006228	biological_process	UTP biosynthetic process
F	0006241	biological_process	CTP biosynthetic process
F	0009117	biological_process	nucleotide metabolic process
F	0016301	molecular_function	kinase activity
F	0046872	molecular_function	metal ion binding
G	0004550	molecular_function	nucleoside diphosphate kinase activity
G	0005524	molecular_function	ATP binding
G	0006183	biological_process	GTP biosynthetic process
G	0006228	biological_process	UTP biosynthetic process
G	0006241	biological_process	CTP biosynthetic process
G	0009117	biological_process	nucleotide metabolic process
G	0016301	molecular_function	kinase activity
G	0046872	molecular_function	metal ion binding
H	0004550	molecular_function	nucleoside diphosphate kinase activity
H	0005524	molecular_function	ATP binding
H	0006183	biological_process	GTP biosynthetic process
H	0006228	biological_process	UTP biosynthetic process
H	0006241	biological_process	CTP biosynthetic process
H	0009117	biological_process	nucleotide metabolic process
H	0016301	molecular_function	kinase activity
H	0046872	molecular_function	metal ion binding
I	0004550	molecular_function	nucleoside diphosphate kinase activity
I	0005524	molecular_function	ATP binding
I	0006183	biological_process	GTP biosynthetic process
I	0006228	biological_process	UTP biosynthetic process
I	0006241	biological_process	CTP biosynthetic process
I	0009117	biological_process	nucleotide metabolic process
I	0016301	molecular_function	kinase activity
I	0046872	molecular_function	metal ion binding
J	0004550	molecular_function	nucleoside diphosphate kinase activity
J	0005524	molecular_function	ATP binding
J	0006183	biological_process	GTP biosynthetic process
J	0006228	biological_process	UTP biosynthetic process
J	0006241	biological_process	CTP biosynthetic process
J	0009117	biological_process	nucleotide metabolic process
J	0016301	molecular_function	kinase activity
J	0046872	molecular_function	metal ion binding
K	0004550	molecular_function	nucleoside diphosphate kinase activity
K	0005524	molecular_function	ATP binding
K	0006183	biological_process	GTP biosynthetic process
K	0006228	biological_process	UTP biosynthetic process
K	0006241	biological_process	CTP biosynthetic process
K	0009117	biological_process	nucleotide metabolic process
K	0016301	molecular_function	kinase activity
K	0046872	molecular_function	metal ion binding
L	0004550	molecular_function	nucleoside diphosphate kinase activity
L	0005524	molecular_function	ATP binding
L	0006183	biological_process	GTP biosynthetic process
L	0006228	biological_process	UTP biosynthetic process
L	0006241	biological_process	CTP biosynthetic process
L	0009117	biological_process	nucleotide metabolic process
L	0016301	molecular_function	kinase activity
L	0046872	molecular_function	metal ion binding

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ASN115-VAL123

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000250

Chain	Residue	Details
A	HIS118
J	HIS118
K	HIS118
L	HIS118
B	HIS118
C	HIS118
D	HIS118
E	HIS118
F	HIS118
G	HIS118
H	HIS118
I	HIS118

site_id	SWS_FT_FI2
Number of Residues	72
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	LYS12
B	THR94
B	ARG105
B	ASN115
C	LYS12
C	PHE60
C	ARG88
C	THR94
C	ARG105
C	ASN115
D	LYS12
A	PHE60
D	PHE60
D	ARG88
D	THR94
D	ARG105
D	ASN115
E	LYS12
E	PHE60
E	ARG88
E	THR94
E	ARG105
A	ARG88
E	ASN115
F	LYS12
F	PHE60
F	ARG88
F	THR94
F	ARG105
F	ASN115
G	LYS12
G	PHE60
G	ARG88
A	THR94
G	THR94
G	ARG105
G	ASN115
H	LYS12
H	PHE60
H	ARG88
H	THR94
H	ARG105
H	ASN115
I	LYS12
A	ARG105
I	PHE60
I	ARG88
I	THR94
I	ARG105
I	ASN115
J	LYS12
J	PHE60
J	ARG88
J	THR94
J	ARG105
A	ASN115
J	ASN115
K	LYS12
K	PHE60
K	ARG88
K	THR94
K	ARG105
K	ASN115
L	LYS12
L	PHE60
L	ARG88
B	LYS12
L	THR94
L	ARG105
L	ASN115
B	PHE60
B	ARG88

Catalytic Information from CSA

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

Chain	Residue	Details
A	ASN115
A	LYS12

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

Chain	Residue	Details
J	ASN115
J	LYS12

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

Chain	Residue	Details
K	ASN115
K	LYS12

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

Chain	Residue	Details
L	ASN115
L	LYS12

site_id	CSA13
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
A	TYR52
A	LYS12

site_id	CSA14
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
B	TYR52
B	LYS12

site_id	CSA15
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
C	TYR52
C	LYS12

site_id	CSA16
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
D	TYR52
D	LYS12

site_id	CSA17
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
E	TYR52
E	LYS12

site_id	CSA18
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
F	TYR52
F	LYS12

site_id	CSA19
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
G	TYR52
G	LYS12

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

Chain	Residue	Details
B	ASN115
B	LYS12

site_id	CSA20
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
H	TYR52
H	LYS12

site_id	CSA21
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
I	TYR52
I	LYS12

site_id	CSA22
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
J	TYR52
J	LYS12

site_id	CSA23
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
K	TYR52
K	LYS12

site_id	CSA24
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
L	TYR52
L	LYS12

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

Chain	Residue	Details
C	ASN115
C	LYS12

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

Chain	Residue	Details
D	ASN115
D	LYS12

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

Chain	Residue	Details
E	ASN115
E	LYS12

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

Chain	Residue	Details
F	ASN115
F	LYS12

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

Chain	Residue	Details
G	ASN115
G	LYS12

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

Chain	Residue	Details
H	ASN115
H	LYS12

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

Chain	Residue	Details
I	ASN115
I	LYS12

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)