Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3GP9

Crystal structure of the Mimivirus NDK complexed with GDP

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	9
Details	BINDING SITE FOR RESIDUE GDP A 138

Chain	Residue
A	LYS9
A	TYR50
A	TYR58
A	ARG99
A	ILE106
A	ARG107
A	ASN109
A	HIS112
A	MG140

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 A 139

Chain	Residue
A	ASN91
A	ILE92
A	ARG99
A	ASN109
A	HOH274

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 140

Chain	Residue
A	GLN89
A	HIS112
A	ALA113
A	GDP138
A	HOH376

site_id	AC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE GDP B 138

Chain	Residue
B	LYS9
B	TYR50
B	HIS53
B	TYR58
B	ASN62
B	ARG86
B	GLN89
B	ARG99
B	ILE106
B	ARG107
B	ASN109
B	HIS112
B	MG140

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 B 139

Chain	Residue
B	ASN91
B	ILE92
B	ARG99
B	ASP105
B	ASN109

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 140

Chain	Residue
B	ARG86
B	GLN89
B	HIS112
B	ALA113
B	GDP138

site_id	AC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GDP C 138

Chain	Residue
C	LYS9
C	TYR50
C	TYR58
C	ARG86
C	GLN89
C	ARG99
C	ILE106
C	ARG107
C	HIS112
C	MG140
C	HOH648

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 C 139

Chain	Residue
C	ASN91
C	ILE92
C	ARG99
C	ASN109

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 140

Chain	Residue
C	ARG86
C	GLN89
C	HIS112
C	ALA113
C	GDP138

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GDP D 138

Chain	Residue
D	LYS9
D	TYR50
D	TYR58
D	ARG99
D	ILE106
D	ASN109
D	HIS112
D	MG140
D	HOH171

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PO4 D 139

Chain	Residue
D	ASN91
D	ILE92
D	ARG99
D	ILE106
D	ASN109
D	HOH382

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 140

Chain	Residue
D	GLN89
D	ARG99
D	HIS112
D	ALA113
D	GDP138

site_id	BC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE GDP E 138

Chain	Residue
E	LYS9
E	TYR50
E	HIS53
E	TYR58
E	ASN62
E	ARG86
E	ARG99
E	ILE106
E	ARG107
E	ASN109
E	HIS112
E	PO4139
E	MG140

site_id	BC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 E 139

Chain	Residue
E	GDP138
E	HOH624
E	HOH644
E	ASN91
E	ILE92
E	ARG99
E	ASN109

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 140

Chain	Residue
E	ARG86
E	GLN89
E	ARG99
E	HIS112
E	ALA113
E	GDP138

site_id	BC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE GDP F 138

Chain	Residue
F	LYS9
F	TYR50
F	HIS53
F	TYR58
F	ARG86
F	GLN89
F	ARG99
F	ILE106
F	ARG107
F	ASN109
F	HIS112
F	MG140
F	HOH664

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PO4 F 139

Chain	Residue
F	ASN91
F	ILE92
F	ARG99
F	ASN109
F	HOH380
F	HOH664

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG F 140

Chain	Residue
F	ARG86
F	GLN89
F	HIS112
F	ALA113
F	GDP138

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)