Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3B6B

Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with dGDP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
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	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0016301	molecular_function	kinase activity
A	0016310	biological_process	phosphorylation
A	0016740	molecular_function	transferase activity
A	0046872	molecular_function	metal ion binding
B	0000166	molecular_function	nucleotide 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	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0016301	molecular_function	kinase activity
B	0016310	biological_process	phosphorylation
B	0016740	molecular_function	transferase activity
B	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide 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	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0016301	molecular_function	kinase activity
C	0016310	biological_process	phosphorylation
C	0016740	molecular_function	transferase activity
C	0046872	molecular_function	metal ion binding
D	0000166	molecular_function	nucleotide 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	0009142	biological_process	nucleoside triphosphate biosynthetic process
D	0016301	molecular_function	kinase activity
D	0016310	biological_process	phosphorylation
D	0016740	molecular_function	transferase activity
D	0046872	molecular_function	metal ion binding
E	0000166	molecular_function	nucleotide 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	0009142	biological_process	nucleoside triphosphate biosynthetic process
E	0016301	molecular_function	kinase activity
E	0016310	biological_process	phosphorylation
E	0016740	molecular_function	transferase activity
E	0046872	molecular_function	metal ion binding
F	0000166	molecular_function	nucleotide 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	0009142	biological_process	nucleoside triphosphate biosynthetic process
F	0016301	molecular_function	kinase activity
F	0016310	biological_process	phosphorylation
F	0016740	molecular_function	transferase activity
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG A 138

Chain	Residue
A	ARG86
A	ARG99

site_id	AC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG B 138

Chain	Residue
B	HIS53

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG D 138

Chain	Residue
D	ARG86
D	ARG99

site_id	AC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE DGI A 139

Chain	Residue
A	ARG86
A	ARG99
A	ILE106
A	ARG107
A	ASN109
A	ASP115
A	HOH181
A	LYS9
A	HIS53
A	TYR58
A	ASN62

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE DGI B 140

Chain	Residue
B	LYS9
B	TYR50
B	HIS53
B	TYR58
B	ARG86
B	ARG99
B	ILE106
B	ARG107
B	ASN109
B	HIS112

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DGI C 141

Chain	Residue
C	LYS9
C	TYR50
C	HIS53
C	TYR58
C	ASN62
C	ARG86
C	ARG99
C	ILE106
C	ARG107
C	ASN109
C	HIS112
C	HOH185

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE DGI D 142

Chain	Residue
D	LYS9
D	HIS53
D	TYR58
D	ASN62
D	ARG86
D	ARG99
D	ILE106
D	ARG107
D	ASN109

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE DGI E 143

Chain	Residue
E	LYS9
E	HIS53
E	TYR58
E	ASN62
E	ARG86
E	ARG99
E	ILE106
E	ARG107
E	ASN109
E	HOH202

site_id	AC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DGI F 144

Chain	Residue
F	LYS9
F	TYR50
F	HIS53
F	TYR58
F	ASN62
F	ARG86
F	GLN89
F	ARG99
F	ILE106
F	ARG107
F	ASN109
F	HIS112

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ASN109-GLU117

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000255\|PROSITE-ProRule:PRU10030

Chain	Residue	Details
A	HIS112
B	HIS112
C	HIS112
D	HIS112
E	HIS112
F	HIS112

site_id	SWS_FT_FI2
Number of Residues	30
Details	BINDING:

Chain	Residue	Details
A	LYS9
B	ASN109
C	LYS9
C	TYR58
C	ARG86
C	ARG99
C	ASN109
D	LYS9
D	TYR58
D	ARG86
D	ARG99
A	TYR58
D	ASN109
E	LYS9
E	TYR58
E	ARG86
E	ARG99
E	ASN109
F	LYS9
F	TYR58
F	ARG86
F	ARG99
A	ARG86
F	ASN109
A	ARG99
A	ASN109
B	LYS9
B	TYR58
B	ARG86
B	ARG99

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