Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3FBB

Crystal structure of the Mimivirus NDK N62L-R107G double mutant 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	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	4
Details	BINDING SITE FOR RESIDUE MG A 202

Chain	Residue
A	ARG86
A	ASP115
A	HOH171
A	UDP201

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE UDP A 201

Chain	Residue
A	GLN89
A	ARG99
A	ILE106
A	GLY107
A	ASN109
A	HOH156
A	HOH171
A	MG202
A	LYS9
A	HIS53
A	TYR58
A	LEU62
A	ARG86

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG B 202

Chain	Residue
B	UDP201

site_id	AC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE UDP B 201

Chain	Residue
B	LYS9
B	TYR50
B	HIS53
B	TYR58
B	LEU62
B	ARG86
B	ARG99
B	ILE106
B	GLY107
B	ASN109
B	HOH147
B	MG202

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG C 202

Chain	Residue
C	ARG86
C	ASP115
C	UDP201

site_id	AC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE UDP C 201

Chain	Residue
C	LYS9
C	HIS53
C	TYR58
C	LEU62
C	ARG86
C	GLN89
C	ARG99
C	ILE106
C	GLY107
C	ASN109
C	HOH156
C	HOH165
C	MG202

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG D 202

Chain	Residue
D	ASP115
D	UDP201

site_id	AC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE UDP D 201

Chain	Residue
D	LYS9
D	HIS53
D	TYR58
D	LEU62
D	ARG86
D	ARG99
D	ILE106
D	GLY107
D	ASN109
D	HOH159
D	MG202

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG E 202

Chain	Residue
E	ARG86
E	ASP115
E	UDP201

site_id	BC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE UDP E 201

Chain	Residue
E	LYS9
E	HIS53
E	TYR58
E	LEU62
E	ARG86
E	ARG99
E	ILE106
E	GLY107
E	ASN109
E	HOH148
E	MG202

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG F 202

Chain	Residue
F	ARG86
F	ASP115
F	UDP201

site_id	BC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE UDP F 201

Chain	Residue
F	LYS9
F	HIS53
F	LEU62
F	ARG86
F	ARG99
F	ILE106
F	GLY107
F	ASN109
F	HOH158
F	MG202

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)