6AY1

Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori

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	0005737	cellular_component	cytoplasm
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	0005737	cellular_component	cytoplasm
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	0005737	cellular_component	cytoplasm
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	0005737	cellular_component	cytoplasm
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	0005737	cellular_component	cytoplasm
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	0005737	cellular_component	cytoplasm
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
G	0000166	molecular_function	nucleotide binding
G	0004550	molecular_function	nucleoside diphosphate kinase activity
G	0005524	molecular_function	ATP binding
G	0005737	cellular_component	cytoplasm
G	0006183	biological_process	GTP biosynthetic process
G	0006228	biological_process	UTP biosynthetic process
G	0006241	biological_process	CTP biosynthetic process
G	0009117	biological_process	nucleotide metabolic process
G	0016301	molecular_function	kinase activity
G	0016740	molecular_function	transferase activity
G	0046872	molecular_function	metal ion binding
H	0000166	molecular_function	nucleotide binding
H	0004550	molecular_function	nucleoside diphosphate kinase activity
H	0005524	molecular_function	ATP binding
H	0005737	cellular_component	cytoplasm
H	0006183	biological_process	GTP biosynthetic process
H	0006228	biological_process	UTP biosynthetic process
H	0006241	biological_process	CTP biosynthetic process
H	0009117	biological_process	nucleotide metabolic process
H	0016301	molecular_function	kinase activity
H	0016740	molecular_function	transferase activity
H	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	binding site for residue IPA A 201

Chain	Residue
A	LYS16
A	LYS17
A	LYS21

---

site_id	AC2
Number of Residues	5
Details	binding site for residue IPA B 201

Chain	Residue
A	LEU96
B	LEU41
B	VAL67
B	HOH350
B	HOH396

---

site_id	AC3
Number of Residues	4
Details	binding site for residue MPD B 202

Chain	Residue
B	LEU62
B	ILE110
B	HOH348
B	PHE58

---

site_id	AC4
Number of Residues	3
Details	binding site for residue HEZ C 201

Chain	Residue
C	LYS10
C	ASN113
C	HOH319

---

site_id	AC5
Number of Residues	4
Details	binding site for residue MPD D 201

Chain	Residue
D	HIS53
D	THR92
D	ARG103
D	HOH324

---

site_id	AC6
Number of Residues	5
Details	binding site for residue HEZ H 201

Chain	Residue
H	LYS10
H	PHE58
H	THR92
H	ILE110
H	ASN113

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ASN113-LEU121

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"source":"HAMAP-Rule","id":"MF_00451","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	45
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00451","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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