Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3EE3

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

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	0016301	molecular_function	kinase activity
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	0016301	molecular_function	kinase activity
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	0016301	molecular_function	kinase activity
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	0016301	molecular_function	kinase activity
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	0016301	molecular_function	kinase activity
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	0016301	molecular_function	kinase activity
F	0016740	molecular_function	transferase activity
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE CDP A 160

Chain	Residue
A	LYS9
A	MG161
A	HOH175
A	HIS53
A	TYR58
A	ASN62
A	ARG86
A	ARG99
A	ILE106
A	ARG107
A	ASN109

site_id	AC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG A 161

Chain	Residue
A	CDP160

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE CDP B 161

Chain	Residue
B	LYS9
B	TYR50
B	HIS53
B	TYR58
B	ASN62
B	ARG86
B	ARG99
B	ILE106
B	ARG107
B	ASN109
B	MG162

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG B 162

Chain	Residue
B	ARG86
B	CDP161

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CDP C 162

Chain	Residue
C	LYS9
C	HIS53
C	TYR58
C	ASN62
C	ARG86
C	ARG99
C	ILE106
C	ARG107
C	ASN109
C	MG163

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG C 163

Chain	Residue
C	CDP162

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CDP D 163

Chain	Residue
D	LYS9
D	TYR50
D	HIS53
D	TYR58
D	ASN62
D	ARG86
D	ARG99
D	ILE106
D	ARG107
D	ASN109
D	MG164
D	HOH176

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG D 164

Chain	Residue
D	CDP163

site_id	AC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CDP E 164

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

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG E 165

Chain	Residue
E	ARG86
E	CDP164

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CDP F 165

Chain	Residue
F	LYS9
F	HIS53
F	TYR58
F	ASN62
F	ARG86
F	ARG99
F	ILE106
F	ARG107
F	ASN109
F	MG166

site_id	BC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG F 166

Chain	Residue
F	CDP165

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	Active site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10030","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	30
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	ASN109
A	LYS9

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

Chain	Residue	Details
D	TYR50
D	LYS9

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

Chain	Residue	Details
E	TYR50
E	LYS9

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

Chain	Residue	Details
F	TYR50
F	LYS9

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

Chain	Residue	Details
B	ASN109
B	LYS9

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

Chain	Residue	Details
C	ASN109
C	LYS9

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

Chain	Residue	Details
D	ASN109
D	LYS9

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

Chain	Residue	Details
E	ASN109
E	LYS9

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

Chain	Residue	Details
F	ASN109
F	LYS9

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

Chain	Residue	Details
A	TYR50
A	LYS9

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

Chain	Residue	Details
B	TYR50
B	LYS9

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

Chain	Residue	Details
C	TYR50
C	LYS9

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