8PYW

Crystal structure of the human Nucleoside-diphosphate kinase B domain bound to compound diphosphate form of AT-9052-Sp.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000155	molecular_function	phosphorelay sensor kinase activity
A	0000160	biological_process	phosphorelay signal transduction system
A	0001726	cellular_component	ruffle
A	0003677	molecular_function	DNA binding
A	0003713	molecular_function	transcription coactivator activity
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005576	cellular_component	extracellular region
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005925	cellular_component	focal adhesion
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0007155	biological_process	cell adhesion
A	0007229	biological_process	integrin-mediated signaling pathway
A	0009117	biological_process	nucleotide metabolic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0016301	molecular_function	kinase activity
A	0019003	molecular_function	GDP binding
A	0030027	cellular_component	lamellipodium
A	0034774	cellular_component	secretory granule lumen
A	0042802	molecular_function	identical protein binding
A	0042981	biological_process	regulation of apoptotic process
A	0042995	cellular_component	cell projection
A	0043066	biological_process	negative regulation of apoptotic process
A	0045618	biological_process	positive regulation of keratinocyte differentiation
A	0045682	biological_process	regulation of epidermis development
A	0045893	biological_process	positive regulation of DNA-templated transcription
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
A	0048471	cellular_component	perinuclear region of cytoplasm
A	0050679	biological_process	positive regulation of epithelial cell proliferation
A	0051880	molecular_function	G-quadruplex DNA binding
A	0070062	cellular_component	extracellular exosome
A	0071944	cellular_component	cell periphery
A	1904813	cellular_component	ficolin-1-rich granule lumen
B	0000155	molecular_function	phosphorelay sensor kinase activity
B	0000160	biological_process	phosphorelay signal transduction system
B	0001726	cellular_component	ruffle
B	0003677	molecular_function	DNA binding
B	0003713	molecular_function	transcription coactivator activity
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005576	cellular_component	extracellular region
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005925	cellular_component	focal adhesion
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0007155	biological_process	cell adhesion
B	0007229	biological_process	integrin-mediated signaling pathway
B	0009117	biological_process	nucleotide metabolic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0016301	molecular_function	kinase activity
B	0019003	molecular_function	GDP binding
B	0030027	cellular_component	lamellipodium
B	0034774	cellular_component	secretory granule lumen
B	0042802	molecular_function	identical protein binding
B	0042981	biological_process	regulation of apoptotic process
B	0042995	cellular_component	cell projection
B	0043066	biological_process	negative regulation of apoptotic process
B	0045618	biological_process	positive regulation of keratinocyte differentiation
B	0045682	biological_process	regulation of epidermis development
B	0045893	biological_process	positive regulation of DNA-templated transcription
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0046872	molecular_function	metal ion binding
B	0048471	cellular_component	perinuclear region of cytoplasm
B	0050679	biological_process	positive regulation of epithelial cell proliferation
B	0051880	molecular_function	G-quadruplex DNA binding
B	0070062	cellular_component	extracellular exosome
B	0071944	cellular_component	cell periphery
B	1904813	cellular_component	ficolin-1-rich granule lumen
C	0000155	molecular_function	phosphorelay sensor kinase activity
C	0000160	biological_process	phosphorelay signal transduction system
C	0001726	cellular_component	ruffle
C	0003677	molecular_function	DNA binding
C	0003713	molecular_function	transcription coactivator activity
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005576	cellular_component	extracellular region
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005925	cellular_component	focal adhesion
C	0006183	biological_process	GTP biosynthetic process
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
C	0007155	biological_process	cell adhesion
C	0007229	biological_process	integrin-mediated signaling pathway
C	0009117	biological_process	nucleotide metabolic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0016301	molecular_function	kinase activity
C	0019003	molecular_function	GDP binding
C	0030027	cellular_component	lamellipodium
C	0034774	cellular_component	secretory granule lumen
C	0042802	molecular_function	identical protein binding
C	0042981	biological_process	regulation of apoptotic process
C	0042995	cellular_component	cell projection
C	0043066	biological_process	negative regulation of apoptotic process
C	0045618	biological_process	positive regulation of keratinocyte differentiation
C	0045682	biological_process	regulation of epidermis development
C	0045893	biological_process	positive regulation of DNA-templated transcription
C	0045944	biological_process	positive regulation of transcription by RNA polymerase II
C	0046872	molecular_function	metal ion binding
C	0048471	cellular_component	perinuclear region of cytoplasm
C	0050679	biological_process	positive regulation of epithelial cell proliferation
C	0051880	molecular_function	G-quadruplex DNA binding
C	0070062	cellular_component	extracellular exosome
C	0071944	cellular_component	cell periphery
C	1904813	cellular_component	ficolin-1-rich granule lumen
D	0000155	molecular_function	phosphorelay sensor kinase activity
D	0000160	biological_process	phosphorelay signal transduction system
D	0001726	cellular_component	ruffle
D	0003677	molecular_function	DNA binding
D	0003713	molecular_function	transcription coactivator activity
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005576	cellular_component	extracellular region
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005925	cellular_component	focal adhesion
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
D	0007155	biological_process	cell adhesion
D	0007229	biological_process	integrin-mediated signaling pathway
D	0009117	biological_process	nucleotide metabolic process
D	0009142	biological_process	nucleoside triphosphate biosynthetic process
D	0016301	molecular_function	kinase activity
D	0019003	molecular_function	GDP binding
D	0030027	cellular_component	lamellipodium
D	0034774	cellular_component	secretory granule lumen
D	0042802	molecular_function	identical protein binding
D	0042981	biological_process	regulation of apoptotic process
D	0042995	cellular_component	cell projection
D	0043066	biological_process	negative regulation of apoptotic process
D	0045618	biological_process	positive regulation of keratinocyte differentiation
D	0045682	biological_process	regulation of epidermis development
D	0045893	biological_process	positive regulation of DNA-templated transcription
D	0045944	biological_process	positive regulation of transcription by RNA polymerase II
D	0046872	molecular_function	metal ion binding
D	0048471	cellular_component	perinuclear region of cytoplasm
D	0050679	biological_process	positive regulation of epithelial cell proliferation
D	0051880	molecular_function	G-quadruplex DNA binding
D	0070062	cellular_component	extracellular exosome
D	0071944	cellular_component	cell periphery
D	1904813	cellular_component	ficolin-1-rich granule lumen
E	0000155	molecular_function	phosphorelay sensor kinase activity
E	0000160	biological_process	phosphorelay signal transduction system
E	0001726	cellular_component	ruffle
E	0003677	molecular_function	DNA binding
E	0003713	molecular_function	transcription coactivator activity
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005576	cellular_component	extracellular region
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0005925	cellular_component	focal adhesion
E	0006183	biological_process	GTP biosynthetic process
E	0006228	biological_process	UTP biosynthetic process
E	0006241	biological_process	CTP biosynthetic process
E	0007155	biological_process	cell adhesion
E	0007229	biological_process	integrin-mediated signaling pathway
E	0009117	biological_process	nucleotide metabolic process
E	0009142	biological_process	nucleoside triphosphate biosynthetic process
E	0016301	molecular_function	kinase activity
E	0019003	molecular_function	GDP binding
E	0030027	cellular_component	lamellipodium
E	0034774	cellular_component	secretory granule lumen
E	0042802	molecular_function	identical protein binding
E	0042981	biological_process	regulation of apoptotic process
E	0042995	cellular_component	cell projection
E	0043066	biological_process	negative regulation of apoptotic process
E	0045618	biological_process	positive regulation of keratinocyte differentiation
E	0045682	biological_process	regulation of epidermis development
E	0045893	biological_process	positive regulation of DNA-templated transcription
E	0045944	biological_process	positive regulation of transcription by RNA polymerase II
E	0046872	molecular_function	metal ion binding
E	0048471	cellular_component	perinuclear region of cytoplasm
E	0050679	biological_process	positive regulation of epithelial cell proliferation
E	0051880	molecular_function	G-quadruplex DNA binding
E	0070062	cellular_component	extracellular exosome
E	0071944	cellular_component	cell periphery
E	1904813	cellular_component	ficolin-1-rich granule lumen
F	0000155	molecular_function	phosphorelay sensor kinase activity
F	0000160	biological_process	phosphorelay signal transduction system
F	0001726	cellular_component	ruffle
F	0003677	molecular_function	DNA binding
F	0003713	molecular_function	transcription coactivator activity
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005576	cellular_component	extracellular region
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0005925	cellular_component	focal adhesion
F	0006183	biological_process	GTP biosynthetic process
F	0006228	biological_process	UTP biosynthetic process
F	0006241	biological_process	CTP biosynthetic process
F	0007155	biological_process	cell adhesion
F	0007229	biological_process	integrin-mediated signaling pathway
F	0009117	biological_process	nucleotide metabolic process
F	0009142	biological_process	nucleoside triphosphate biosynthetic process
F	0016301	molecular_function	kinase activity
F	0019003	molecular_function	GDP binding
F	0030027	cellular_component	lamellipodium
F	0034774	cellular_component	secretory granule lumen
F	0042802	molecular_function	identical protein binding
F	0042981	biological_process	regulation of apoptotic process
F	0042995	cellular_component	cell projection
F	0043066	biological_process	negative regulation of apoptotic process
F	0045618	biological_process	positive regulation of keratinocyte differentiation
F	0045682	biological_process	regulation of epidermis development
F	0045893	biological_process	positive regulation of DNA-templated transcription
F	0045944	biological_process	positive regulation of transcription by RNA polymerase II
F	0046872	molecular_function	metal ion binding
F	0048471	cellular_component	perinuclear region of cytoplasm
F	0050679	biological_process	positive regulation of epithelial cell proliferation
F	0051880	molecular_function	G-quadruplex DNA binding
F	0070062	cellular_component	extracellular exosome
F	0071944	cellular_component	cell periphery
F	1904813	cellular_component	ficolin-1-rich granule lumen

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

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000269|PubMed:1851158

Chain	Residue	Details
A	HIS122
B	HIS122
C	HIS122
D	HIS122
E	HIS122
F	HIS122

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site_id	SWS_FT_FI2
Number of Residues	36
Details	BINDING: BINDING => ECO:0000269|PubMed:19435876, ECO:0007744|PDB:3BBF

Chain	Residue	Details
A	LYS16
B	THR98
B	ARG109
B	ASN119
C	LYS16
C	PHE64
C	ARG92
C	THR98
C	ARG109
C	ASN119
D	LYS16
A	PHE64
D	PHE64
D	ARG92
D	THR98
D	ARG109
D	ASN119
E	LYS16
E	PHE64
E	ARG92
E	THR98
E	ARG109
A	ARG92
E	ASN119
F	LYS16
F	PHE64
F	ARG92
F	THR98
F	ARG109
F	ASN119
A	THR98
A	ARG109
A	ASN119
B	LYS16
B	PHE64
B	ARG92

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