Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3NGT

Structure of Leishmania NDKb complexed with AMP.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0016301	molecular_function	kinase activity
A	0016310	biological_process	phosphorylation
A	0097014	cellular_component	ciliary plasm
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0016301	molecular_function	kinase activity
B	0016310	biological_process	phosphorylation
B	0097014	cellular_component	ciliary plasm
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0006183	biological_process	GTP biosynthetic process
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0016301	molecular_function	kinase activity
C	0016310	biological_process	phosphorylation
C	0097014	cellular_component	ciliary plasm
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
D	0009142	biological_process	nucleoside triphosphate biosynthetic process
D	0016301	molecular_function	kinase activity
D	0016310	biological_process	phosphorylation
D	0097014	cellular_component	ciliary plasm
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0005524	molecular_function	ATP binding
E	0005737	cellular_component	cytoplasm
E	0006183	biological_process	GTP biosynthetic process
E	0006228	biological_process	UTP biosynthetic process
E	0006241	biological_process	CTP biosynthetic process
E	0009142	biological_process	nucleoside triphosphate biosynthetic process
E	0016301	molecular_function	kinase activity
E	0016310	biological_process	phosphorylation
E	0097014	cellular_component	ciliary plasm
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0005524	molecular_function	ATP binding
F	0005737	cellular_component	cytoplasm
F	0006183	biological_process	GTP biosynthetic process
F	0006228	biological_process	UTP biosynthetic process
F	0006241	biological_process	CTP biosynthetic process
F	0009142	biological_process	nucleoside triphosphate biosynthetic process
F	0016301	molecular_function	kinase activity
F	0016310	biological_process	phosphorylation
F	0097014	cellular_component	ciliary plasm
G	0004550	molecular_function	nucleoside diphosphate kinase activity
G	0005524	molecular_function	ATP binding
G	0005737	cellular_component	cytoplasm
G	0006183	biological_process	GTP biosynthetic process
G	0006228	biological_process	UTP biosynthetic process
G	0006241	biological_process	CTP biosynthetic process
G	0009142	biological_process	nucleoside triphosphate biosynthetic process
G	0016301	molecular_function	kinase activity
G	0016310	biological_process	phosphorylation
G	0097014	cellular_component	ciliary plasm
H	0004550	molecular_function	nucleoside diphosphate kinase activity
H	0005524	molecular_function	ATP binding
H	0005737	cellular_component	cytoplasm
H	0006183	biological_process	GTP biosynthetic process
H	0006228	biological_process	UTP biosynthetic process
H	0006241	biological_process	CTP biosynthetic process
H	0009142	biological_process	nucleoside triphosphate biosynthetic process
H	0016301	molecular_function	kinase activity
H	0016310	biological_process	phosphorylation
H	0097014	cellular_component	ciliary plasm
I	0004550	molecular_function	nucleoside diphosphate kinase activity
I	0005524	molecular_function	ATP binding
I	0005737	cellular_component	cytoplasm
I	0006183	biological_process	GTP biosynthetic process
I	0006228	biological_process	UTP biosynthetic process
I	0006241	biological_process	CTP biosynthetic process
I	0009142	biological_process	nucleoside triphosphate biosynthetic process
I	0016301	molecular_function	kinase activity
I	0016310	biological_process	phosphorylation
I	0097014	cellular_component	ciliary plasm
J	0004550	molecular_function	nucleoside diphosphate kinase activity
J	0005524	molecular_function	ATP binding
J	0005737	cellular_component	cytoplasm
J	0006183	biological_process	GTP biosynthetic process
J	0006228	biological_process	UTP biosynthetic process
J	0006241	biological_process	CTP biosynthetic process
J	0009142	biological_process	nucleoside triphosphate biosynthetic process
J	0016301	molecular_function	kinase activity
J	0016310	biological_process	phosphorylation
J	0097014	cellular_component	ciliary plasm
K	0004550	molecular_function	nucleoside diphosphate kinase activity
K	0005524	molecular_function	ATP binding
K	0005737	cellular_component	cytoplasm
K	0006183	biological_process	GTP biosynthetic process
K	0006228	biological_process	UTP biosynthetic process
K	0006241	biological_process	CTP biosynthetic process
K	0009142	biological_process	nucleoside triphosphate biosynthetic process
K	0016301	molecular_function	kinase activity
K	0016310	biological_process	phosphorylation
K	0097014	cellular_component	ciliary plasm
L	0004550	molecular_function	nucleoside diphosphate kinase activity
L	0005524	molecular_function	ATP binding
L	0005737	cellular_component	cytoplasm
L	0006183	biological_process	GTP biosynthetic process
L	0006228	biological_process	UTP biosynthetic process
L	0006241	biological_process	CTP biosynthetic process
L	0009142	biological_process	nucleoside triphosphate biosynthetic process
L	0016301	molecular_function	kinase activity
L	0016310	biological_process	phosphorylation
L	0097014	cellular_component	ciliary plasm
M	0004550	molecular_function	nucleoside diphosphate kinase activity
M	0005524	molecular_function	ATP binding
M	0005737	cellular_component	cytoplasm
M	0006183	biological_process	GTP biosynthetic process
M	0006228	biological_process	UTP biosynthetic process
M	0006241	biological_process	CTP biosynthetic process
M	0009142	biological_process	nucleoside triphosphate biosynthetic process
M	0016301	molecular_function	kinase activity
M	0016310	biological_process	phosphorylation
M	0097014	cellular_component	ciliary plasm
N	0004550	molecular_function	nucleoside diphosphate kinase activity
N	0005524	molecular_function	ATP binding
N	0005737	cellular_component	cytoplasm
N	0006183	biological_process	GTP biosynthetic process
N	0006228	biological_process	UTP biosynthetic process
N	0006241	biological_process	CTP biosynthetic process
N	0009142	biological_process	nucleoside triphosphate biosynthetic process
N	0016301	molecular_function	kinase activity
N	0016310	biological_process	phosphorylation
N	0097014	cellular_component	ciliary plasm

Functional Information from PDB Data

site_id	AC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AMP A 152

Chain	Residue
A	LYS11
A	HOH167
A	HOH197
A	HOH273
A	TYR51
A	LEU54
A	PHE59
A	LEU63
A	THR93
A	VAL111
A	ASN114
A	HIS117

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE AMP B 152

Chain	Residue
B	LYS11
B	TYR51
B	PHE59
B	THR93
B	VAL111
B	ASN114
B	HIS117
B	HOH306
F	GLU151

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE AMP C 152

Chain	Residue
A	GLU151
C	LYS11
C	TYR51
C	LEU54
C	PHE59
C	THR93
C	ARG104
C	VAL111
C	ASN114
C	HIS117

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE AMP D 152

Chain	Residue
D	LYS11
D	TYR51
D	PHE59
D	VAL111
D	ASN114
D	HIS117

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE AMP E 152

Chain	Residue
E	LYS11
E	TYR51
E	LEU54
E	PHE59
E	VAL111
E	ASN114
E	HIS117

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE AMP F 152

Chain	Residue
D	GLU151
F	LYS11
F	TYR51
F	PHE59
F	ARG104
F	VAL111
F	HIS117
F	HOH301

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE AMP G 152

Chain	Residue
G	LYS11
G	TYR51
G	PHE59
G	LEU63
G	THR93
G	VAL111
G	ASN114
G	HIS117
K	GLU151

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE AMP H 152

Chain	Residue
H	LYS11
H	TYR51
H	PHE59
H	VAL111
H	ASN114
H	HIS117
H	HOH158
H	HOH205

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE AMP I 152

Chain	Residue
I	LYS11
I	TYR51
I	PHE59
I	LEU63
I	THR93
I	VAL111
I	ASN114
I	HIS117

site_id	BC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE AMP J 152

Chain	Residue
H	GLU151
J	LYS11
J	TYR51
J	LEU54
J	PHE59
J	THR93
J	ARG104
J	VAL111
J	HIS117
J	HOH156

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE AMP K 152

Chain	Residue
K	LYS11
K	TYR51
K	PHE59
K	LEU63
K	THR93
K	ASN114
K	HIS117

site_id	BC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AMP M 152

Chain	Residue
M	ARG104
M	VAL111
M	ASN114
M	HIS117
M	GLU151
M	HOH211
M	LYS11
M	TYR51
M	LEU54
M	PHE59
M	THR93

site_id	BC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AMP N 152

Chain	Residue
N	LYS11
N	TYR51
N	LEU54
N	PHE59
N	THR93
N	VAL111
N	ASN114
N	HIS117
N	GLU151
N	HOH159
N	HOH162

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ASN114-VAL122

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