Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2BEF

CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3

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	0005840	cellular_component	ribosome
A	0005856	cellular_component	cytoskeleton
A	0005886	cellular_component	plasma membrane
A	0006183	biological_process	GTP biosynthetic process
A	0006187	biological_process	dGTP biosynthetic process from dGDP
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0006414	biological_process	translational elongation
A	0007186	biological_process	G protein-coupled receptor signaling pathway
A	0009117	biological_process	nucleotide metabolic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0009617	biological_process	response to bacterium
A	0015629	cellular_component	actin cytoskeleton
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0019954	biological_process	asexual reproduction
A	0030036	biological_process	actin cytoskeleton organization
A	0030141	cellular_component	secretory granule
A	0045335	cellular_component	phagocytic vesicle
A	0045920	biological_process	negative regulation of exocytosis
A	0046872	molecular_function	metal ion binding
A	0048550	biological_process	negative regulation of pinocytosis
A	0050765	biological_process	negative regulation of phagocytosis
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	0005840	cellular_component	ribosome
B	0005856	cellular_component	cytoskeleton
B	0005886	cellular_component	plasma membrane
B	0006183	biological_process	GTP biosynthetic process
B	0006187	biological_process	dGTP biosynthetic process from dGDP
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0006414	biological_process	translational elongation
B	0007186	biological_process	G protein-coupled receptor signaling pathway
B	0009117	biological_process	nucleotide metabolic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0009617	biological_process	response to bacterium
B	0015629	cellular_component	actin cytoskeleton
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0019954	biological_process	asexual reproduction
B	0030036	biological_process	actin cytoskeleton organization
B	0030141	cellular_component	secretory granule
B	0045335	cellular_component	phagocytic vesicle
B	0045920	biological_process	negative regulation of exocytosis
B	0046872	molecular_function	metal ion binding
B	0048550	biological_process	negative regulation of pinocytosis
B	0050765	biological_process	negative regulation of phagocytosis
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	0005840	cellular_component	ribosome
C	0005856	cellular_component	cytoskeleton
C	0005886	cellular_component	plasma membrane
C	0006183	biological_process	GTP biosynthetic process
C	0006187	biological_process	dGTP biosynthetic process from dGDP
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
C	0006414	biological_process	translational elongation
C	0007186	biological_process	G protein-coupled receptor signaling pathway
C	0009117	biological_process	nucleotide metabolic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0009617	biological_process	response to bacterium
C	0015629	cellular_component	actin cytoskeleton
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0019954	biological_process	asexual reproduction
C	0030036	biological_process	actin cytoskeleton organization
C	0030141	cellular_component	secretory granule
C	0045335	cellular_component	phagocytic vesicle
C	0045920	biological_process	negative regulation of exocytosis
C	0046872	molecular_function	metal ion binding
C	0048550	biological_process	negative regulation of pinocytosis
C	0050765	biological_process	negative regulation of phagocytosis

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 156

Chain	Residue
A	BEF157
A	ADP158
A	HOH619
A	HOH626
A	HOH693

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 156

Chain	Residue
B	HOH779
B	BEF157
B	ADP158
B	HOH620
B	HOH706

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 156

Chain	Residue
C	BEF157
C	ADP158
C	HOH643
C	HOH777
C	HOH778

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE BEF A 157

Chain	Residue
A	LYS16
A	TYR56
A	ARG92
A	ARG109
A	HIS122
A	GLY123
A	MG156
A	ADP158
A	HOH619
A	HOH626

site_id	AC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ADP A 158

Chain	Residue
A	LYS16
A	HIS59
A	PHE64
A	LEU68
A	ARG92
A	THR98
A	ARG109
A	VAL116
A	ASN119
A	MG156
A	BEF157
A	HOH619
A	HOH626
A	HOH681
A	HOH693
A	HOH729

site_id	AC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE BEF B 157

Chain	Residue
B	LYS16
B	TYR56
B	ARG92
B	ARG109
B	HIS122
B	GLY123
B	MG156
B	ADP158
B	HOH620
B	HOH779

site_id	AC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ADP B 158

Chain	Residue
A	LYS60
B	LYS16
B	HIS59
B	PHE64
B	LEU68
B	ARG92
B	THR98
B	ARG109
B	VAL116
B	ASN119
B	MG156
B	BEF157
B	HOH706
B	HOH779
B	HOH802

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE BEF C 157

Chain	Residue
C	LYS16
C	TYR56
C	ARG109
C	HIS122
C	GLY123
C	MG156
C	ADP158
C	HOH643
C	HOH777

site_id	AC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ADP C 158

Chain	Residue
C	LYS16
C	TYR56
C	HIS59
C	PHE64
C	LEU68
C	ARG92
C	THR98
C	ARG109
C	VAL116
C	ASN119
C	MG156
C	BEF157
C	HOH617
C	HOH643
C	HOH778

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ASN119-VAL127

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	Active site: {"description":"Pros-phosphohistidine intermediate"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	18
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	ASN119
A	LYS16

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

Chain	Residue	Details
B	ASN119
B	LYS16

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

Chain	Residue	Details
C	ASN119
C	LYS16

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

Chain	Residue	Details
A	TYR56
A	LYS16

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

Chain	Residue	Details
B	TYR56
B	LYS16

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

Chain	Residue	Details
C	TYR56
C	LYS16

site_id	MCSA1
Number of Residues	5
Details	M-CSA 150

Chain	Residue	Details
A	LYS16	electrostatic stabiliser, hydrogen bond donor
A	TYR56	electrostatic stabiliser, hydrogen bond donor
A	ASN119	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
A	HIS122	hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
A	GLU133	hydrogen bond acceptor, increase nucleophilicity, steric role

site_id	MCSA2
Number of Residues	5
Details	M-CSA 150

Chain	Residue	Details
B	LYS16	electrostatic stabiliser, hydrogen bond donor
B	TYR56	electrostatic stabiliser, hydrogen bond donor
B	ASN119	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
B	HIS122	hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
B	GLU133	hydrogen bond acceptor, increase nucleophilicity, steric role

site_id	MCSA3
Number of Residues	5
Details	M-CSA 150

Chain	Residue	Details
C	LYS16	electrostatic stabiliser, hydrogen bond donor
C	TYR56	electrostatic stabiliser, hydrogen bond donor
C	ASN119	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
C	HIS122	hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
C	GLU133	hydrogen bond acceptor, increase nucleophilicity, steric role

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