Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5U2I

Crystal structure of a nucleoside diphosphate kinase from Naegleria fowleri

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	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	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	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	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	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	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	3
Details	binding site for residue EDO A 201

Chain	Residue
A	ARG5
A	GLU140
A	HOH301

site_id	AC2
Number of Residues	3
Details	binding site for residue EDO B 201

Chain	Residue
B	ARG5
B	GLU140
B	MG203

site_id	AC3
Number of Residues	10
Details	binding site for residue EDO B 202

Chain	Residue
B	GLU137
B	LEU138
B	ASN139
B	HOH317
B	HOH330
B	HOH340
B	HOH347
A	ILE40
A	THR41
B	SER136

site_id	AC4
Number of Residues	7
Details	binding site for residue MG B 203

Chain	Residue
B	ARG5
B	LYS33
B	GLU78
B	EDO201
B	HOH331
B	HOH398
B	HOH399

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO C 201

Chain	Residue
C	ARG5
C	LEU138
C	GLU140
C	HOH336

site_id	AC6
Number of Residues	4
Details	binding site for residue EDO D 201

Chain	Residue
D	ARG5
D	ASN139
D	GLU140
D	HOH432

site_id	AC7
Number of Residues	6
Details	binding site for residue FMT D 202

Chain	Residue
D	ALA130
D	LEU131
D	TRP132
D	PHE133
D	GLN134
D	HOH301

site_id	AC8
Number of Residues	4
Details	binding site for residue MG D 203

Chain	Residue
C	HOH394
D	ASP55
D	GLY56
D	HOH496

site_id	AC9
Number of Residues	6
Details	binding site for residue MG D 204

Chain	Residue
B	HOH547
C	HOH364
D	HOH318
D	HOH330
D	HOH491
D	HOH531

site_id	AD1
Number of Residues	8
Details	binding site for residue EDO D 205

Chain	Residue
D	SER136
D	LEU138
D	ASN139
D	HOH338
D	HOH402
E	ILE40
E	THR41
E	HOH380

site_id	AD2
Number of Residues	5
Details	binding site for residue FMT D 206

Chain	Residue
D	ARG26
D	GLN29
D	HOH305
D	HOH325
D	HOH361

site_id	AD3
Number of Residues	5
Details	binding site for residue EDO E 201

Chain	Residue
E	ARG5
E	ASN139
E	GLU140
E	HOH316
E	HOH439

site_id	AD4
Number of Residues	7
Details	binding site for residue EDO E 202

Chain	Residue
E	ARG104
E	HIS117
E	GLY118
E	FMT203
E	HOH307
E	HOH332
E	HOH422

site_id	AD5
Number of Residues	5
Details	binding site for residue FMT E 203

Chain	Residue
E	LYS11
E	TYR51
E	HIS117
E	EDO202
E	HOH407

site_id	AD6
Number of Residues	7
Details	binding site for residue EDO F 201

Chain	Residue
F	ARG5
F	LEU138
F	ASN139
F	GLU140
F	HOH330
F	HOH332
F	HOH409

site_id	AD7
Number of Residues	7
Details	binding site for residue EDO F 202

Chain	Residue
D	LYS147
F	ASP45
F	LEU46
F	LEU131
F	HOH302
F	HOH447
F	HOH460

site_id	AD8
Number of Residues	9
Details	binding site for residue EDO F 203

Chain	Residue
F	HOH404
C	ILE40
C	THR41
C	HOH451
F	SER136
F	LEU138
F	ASN139
F	HOH306
F	HOH379

site_id	AD9
Number of Residues	8
Details	binding site for residue EDO F 204

Chain	Residue
F	ARG87
F	ARG104
F	HIS117
F	GLY118
F	HOH304
F	HOH309
F	HOH360
F	HOH451

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ASN114-VAL122

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