3BBF

Crystal structure of the NM23-H2 transcription factor complex with GDP

Functional Information from GO Data

Chain	GOid	namespace	contents
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	0004673	molecular_function	protein histidine 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	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	0004673	molecular_function	protein histidine 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	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	0004673	molecular_function	protein histidine 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	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	0004673	molecular_function	protein histidine 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	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	0004673	molecular_function	protein histidine 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	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	0004673	molecular_function	protein histidine 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 PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 161

Chain	Residue
A	GDP160
A	HOH166
A	HOH171
A	HOH215
A	HOH220
A	HOH225

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 161

Chain	Residue
B	HOH220
B	HOH282
B	HOH293
B	GDP160
B	HOH174
B	HOH201

---

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 161

Chain	Residue
C	GDP160
C	HOH170
C	HOH191
C	HOH211
C	HOH214
C	HOH249

---

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 161

Chain	Residue
D	GDP160
D	HOH193
D	HOH221
D	HOH227
D	HOH235
D	HOH257

---

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG E 161

Chain	Residue
E	GDP160
E	HOH173
E	HOH219
E	HOH223

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG F 161

Chain	Residue
F	ASP54
F	GDP160
F	HOH200
F	HOH235
F	HOH242

---

site_id	AC7
Number of Residues	23
Details	BINDING SITE FOR RESIDUE GDP A 160

Chain	Residue
A	LYS12
A	TYR52
A	LEU55
A	PHE60
A	LEU64
A	ARG88
A	THR94
A	VAL112
A	GLY113
A	ASN115
A	MG161
A	HOH166
A	HOH168
A	HOH171
A	HOH197
A	HOH224
A	HOH225
A	HOH232
A	HOH250
A	HOH259
A	HOH298
B	GLU152
B	HOH170

---

site_id	AC8
Number of Residues	18
Details	BINDING SITE FOR RESIDUE GDP B 160

Chain	Residue
B	LYS12
B	TYR52
B	LEU55
B	PHE60
B	LEU64
B	ARG88
B	THR94
B	VAL112
B	GLY113
B	ASN115
B	MG161
B	HOH175
B	HOH190
B	HOH201
B	HOH220
B	HOH221
B	HOH282
C	GLU152

---

site_id	AC9
Number of Residues	22
Details	BINDING SITE FOR RESIDUE GDP C 160

Chain	Residue
A	GLU152
B	ALA2
B	ASN3
C	LYS12
C	TYR52
C	LEU55
C	PHE60
C	LEU64
C	ARG88
C	THR94
C	VAL112
C	GLY113
C	ASN115
C	MG161
C	HOH172
C	HOH185
C	HOH191
C	HOH194
C	HOH198
C	HOH211
C	HOH214
C	HOH258

---

site_id	BC1
Number of Residues	20
Details	BINDING SITE FOR RESIDUE GDP D 160

Chain	Residue
D	PHE60
D	LEU64
D	ARG88
D	THR94
D	VAL112
D	GLY113
D	ASN115
D	MG161
D	HOH169
D	HOH174
D	HOH202
D	HOH221
D	HOH229
D	HOH234
D	HOH235
D	HOH257
F	GLU152
D	LYS12
D	TYR52
D	LEU55

---

site_id	BC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE GDP E 160

Chain	Residue
D	GLU152
E	LYS12
E	TYR52
E	LEU55
E	PHE60
E	LEU64
E	ARG88
E	THR94
E	VAL112
E	ASN115
E	MG161
E	HOH169
E	HOH173
E	HOH215
E	HOH217
E	HOH223
E	HOH228

---

site_id	BC3
Number of Residues	17
Details	BINDING SITE FOR RESIDUE GDP F 160

Chain	Residue
E	GLU152
F	LYS12
F	TYR52
F	LEU55
F	PHE60
F	LEU64
F	ARG88
F	THR94
F	VAL112
F	ASN115
F	MG161
F	HOH170
F	HOH184
F	HOH193
F	HOH227
F	HOH235
F	HOH242

---

site_id	BC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE DTT B 162

Chain	Residue
A	GLN17
A	ARG18
A	GLY19
B	CYS145
B	ALA146
B	HOH199
B	HOH212
B	HOH225
B	HOH226
D	CYS145
D	ALA146
D	HOH215
E	GLN17
E	ARG18
E	GLY19

---

site_id	BC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE DTT F 162

Chain	Residue
B	GLN17
B	ARG18
B	GLY19
C	CYS145
C	ALA146
C	HOH226
C	HOH241
E	GLU29
E	CYS145
E	ALA146
E	HOH164
F	GLN17
F	ARG18
F	GLY19
F	HOH230

---

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	ASN115-VAL123

---

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	HIS118
B	HIS118
C	HIS118
D	HIS118
E	HIS118
F	HIS118

---

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

Chain	Residue	Details
A	LYS12
B	THR94
B	ARG105
B	ASN115
C	LYS12
C	PHE60
C	ARG88
C	THR94
C	ARG105
C	ASN115
D	LYS12
A	PHE60
D	PHE60
D	ARG88
D	THR94
D	ARG105
D	ASN115
E	LYS12
E	PHE60
E	ARG88
E	THR94
E	ARG105
A	ARG88
E	ASN115
F	LYS12
F	PHE60
F	ARG88
F	THR94
F	ARG105
F	ASN115
A	THR94
A	ARG105
A	ASN115
B	LYS12
B	PHE60
B	ARG88

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
A	ASN115
A	LYS12

---

site_id	CSA10
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
D	TYR52
D	LYS12

---

site_id	CSA11
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
E	TYR52
E	LYS12

---

site_id	CSA12
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
F	TYR52
F	LYS12

---

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

Chain	Residue	Details
B	ASN115
B	LYS12

---

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

Chain	Residue	Details
C	ASN115
C	LYS12

---

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

Chain	Residue	Details
D	ASN115
D	LYS12

---

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

Chain	Residue	Details
E	ASN115
E	LYS12

---

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

Chain	Residue	Details
F	ASN115
F	LYS12

---

site_id	CSA7
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
A	TYR52
A	LYS12

---

site_id	CSA8
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
B	TYR52
B	LYS12

---

site_id	CSA9
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
C	TYR52
C	LYS12

---