Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3EIC

X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with UDP

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 160

Chain	Residue
A	ARG86
A	UDP161

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG B 161

Chain	Residue
B	ARG86
B	UDP162

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG C 162

Chain	Residue
C	ARG86
C	UDP163

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG D 163

Chain	Residue
D	UDP164

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG E 164

Chain	Residue
E	UDP165

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG F 165

Chain	Residue
F	UDP166
F	ARG86

site_id	AC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE UDP A 161

Chain	Residue
A	LYS9
A	HIS53
A	TYR58
A	ASN62
A	ARG86
A	GLN89
A	ARG99
A	ILE106
A	ARG107
A	ASN109
A	MG160
A	HOH195
A	HOH196

site_id	AC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE UDP B 162

Chain	Residue
B	LYS9
B	TYR50
B	HIS53
B	TYR58
B	ASN62
B	ARG86
B	ARG99
B	ILE106
B	ARG107
B	ASN109
B	MG161
B	HOH171

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE UDP C 163

Chain	Residue
C	LYS9
C	TYR50
C	HIS53
C	TYR58
C	ASN62
C	ARG86
C	ARG99
C	ILE106
C	ARG107
C	ASN109
C	MG162
C	HOH188
C	HOH207

site_id	BC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE UDP D 164

Chain	Residue
D	LYS9
D	TYR50
D	HIS53
D	TYR58
D	ASN62
D	ARG86
D	GLN89
D	ARG99
D	ILE106
D	ARG107
D	ASN109
D	MG163
D	HOH168
D	HOH198

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE UDP E 165

Chain	Residue
E	LYS9
E	HIS53
E	TYR58
E	ASN62
E	ARG86
E	ARG99
E	ILE106
E	ARG107
E	ASN109
E	MG164
E	HOH171
E	HOH204

site_id	BC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE UDP F 166

Chain	Residue
F	LYS9
F	HIS53
F	TYR58
F	ASN62
F	ARG86
F	ARG99
F	ILE106
F	ARG107
F	ASN109
F	MG165
F	HOH195

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)