Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5UKF

Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004672	molecular_function	protein kinase activity
A	0004674	molecular_function	protein serine/threonine kinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005730	cellular_component	nucleolus
A	0005737	cellular_component	cytoplasm
A	0005795	cellular_component	Golgi stack
A	0005829	cellular_component	cytosol
A	0006338	biological_process	chromatin remodeling
A	0006468	biological_process	protein phosphorylation
A	0006974	biological_process	DNA damage response
A	0007049	biological_process	cell cycle
A	0007077	biological_process	mitotic nuclear membrane disassembly
A	0007165	biological_process	signal transduction
A	0016301	molecular_function	kinase activity
A	0016310	biological_process	phosphorylation
A	0016740	molecular_function	transferase activity
A	0019901	molecular_function	protein kinase binding
A	0035175	molecular_function	histone H3S10 kinase activity
A	0042393	molecular_function	histone binding
A	0046777	biological_process	protein autophosphorylation
A	0051301	biological_process	cell division
A	0072354	molecular_function	histone H3T3 kinase activity
A	0090166	biological_process	Golgi disassembly
A	0106310	molecular_function	protein serine kinase activity
A	0120187	biological_process	positive regulation of protein localization to chromatin
B	0000166	molecular_function	nucleotide binding
B	0004672	molecular_function	protein kinase activity
B	0004674	molecular_function	protein serine/threonine kinase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005730	cellular_component	nucleolus
B	0005737	cellular_component	cytoplasm
B	0005795	cellular_component	Golgi stack
B	0005829	cellular_component	cytosol
B	0006338	biological_process	chromatin remodeling
B	0006468	biological_process	protein phosphorylation
B	0006974	biological_process	DNA damage response
B	0007049	biological_process	cell cycle
B	0007077	biological_process	mitotic nuclear membrane disassembly
B	0007165	biological_process	signal transduction
B	0016301	molecular_function	kinase activity
B	0016310	biological_process	phosphorylation
B	0016740	molecular_function	transferase activity
B	0019901	molecular_function	protein kinase binding
B	0035175	molecular_function	histone H3S10 kinase activity
B	0042393	molecular_function	histone binding
B	0046777	biological_process	protein autophosphorylation
B	0051301	biological_process	cell division
B	0072354	molecular_function	histone H3T3 kinase activity
B	0090166	biological_process	Golgi disassembly
B	0106310	molecular_function	protein serine kinase activity
B	0120187	biological_process	positive regulation of protein localization to chromatin
C	0000166	molecular_function	nucleotide binding
C	0004672	molecular_function	protein kinase activity
C	0004674	molecular_function	protein serine/threonine kinase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005730	cellular_component	nucleolus
C	0005737	cellular_component	cytoplasm
C	0005795	cellular_component	Golgi stack
C	0005829	cellular_component	cytosol
C	0006338	biological_process	chromatin remodeling
C	0006468	biological_process	protein phosphorylation
C	0006974	biological_process	DNA damage response
C	0007049	biological_process	cell cycle
C	0007077	biological_process	mitotic nuclear membrane disassembly
C	0007165	biological_process	signal transduction
C	0016301	molecular_function	kinase activity
C	0016310	biological_process	phosphorylation
C	0016740	molecular_function	transferase activity
C	0019901	molecular_function	protein kinase binding
C	0035175	molecular_function	histone H3S10 kinase activity
C	0042393	molecular_function	histone binding
C	0046777	biological_process	protein autophosphorylation
C	0051301	biological_process	cell division
C	0072354	molecular_function	histone H3T3 kinase activity
C	0090166	biological_process	Golgi disassembly
C	0106310	molecular_function	protein serine kinase activity
C	0120187	biological_process	positive regulation of protein localization to chromatin
D	0000166	molecular_function	nucleotide binding
D	0004672	molecular_function	protein kinase activity
D	0004674	molecular_function	protein serine/threonine kinase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005730	cellular_component	nucleolus
D	0005737	cellular_component	cytoplasm
D	0005795	cellular_component	Golgi stack
D	0005829	cellular_component	cytosol
D	0006338	biological_process	chromatin remodeling
D	0006468	biological_process	protein phosphorylation
D	0006974	biological_process	DNA damage response
D	0007049	biological_process	cell cycle
D	0007077	biological_process	mitotic nuclear membrane disassembly
D	0007165	biological_process	signal transduction
D	0016301	molecular_function	kinase activity
D	0016310	biological_process	phosphorylation
D	0016740	molecular_function	transferase activity
D	0019901	molecular_function	protein kinase binding
D	0035175	molecular_function	histone H3S10 kinase activity
D	0042393	molecular_function	histone binding
D	0046777	biological_process	protein autophosphorylation
D	0051301	biological_process	cell division
D	0072354	molecular_function	histone H3T3 kinase activity
D	0090166	biological_process	Golgi disassembly
D	0106310	molecular_function	protein serine kinase activity
D	0120187	biological_process	positive regulation of protein localization to chromatin

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	binding site for residue 8E1 A 401

Chain	Residue
A	PHE48
A	HOH501
A	VAL69
A	ASP132
A	PHE134
A	GLY135
A	SER136
A	ASP137
A	LYS140
A	LEU184

site_id	AC2
Number of Residues	4
Details	binding site for residue PO4 A 402

Chain	Residue
A	ASP120
A	LYS121
A	ASN122
D	ARG89

site_id	AC3
Number of Residues	2
Details	binding site for residue CL A 403

Chain	Residue
A	ARG148
A	HIS258

site_id	AC4
Number of Residues	7
Details	binding site for residue 8E1 B 401

Chain	Residue
B	MET131
B	ASP132
B	PHE134
B	GLY135
B	SER136
B	ASP137
B	LEU184

site_id	AC5
Number of Residues	2
Details	binding site for residue PO4 B 402

Chain	Residue
B	ARG89
B	ARG203

site_id	AC6
Number of Residues	4
Details	binding site for residue PO4 B 403

Chain	Residue
B	TYR202
B	LYS211
B	ARG219
B	HOH560

site_id	AC7
Number of Residues	2
Details	binding site for residue PO4 B 404

Chain	Residue
B	ARG148
B	HIS258

site_id	AC8
Number of Residues	2
Details	binding site for residue PO4 B 405

Chain	Residue
B	GLN95
B	HIS171

site_id	AC9
Number of Residues	1
Details	binding site for residue CL B 406

Chain	Residue
B	ARG241

site_id	AD1
Number of Residues	9
Details	binding site for residue 8E1 C 401

Chain	Residue
C	PHE48
C	VAL69
C	ASP132
C	PHE134
C	GLY135
C	SER136
C	ASP137
C	LYS140
C	HOH505

site_id	AD2
Number of Residues	8
Details	binding site for residue PO4 C 402

Chain	Residue
C	ARG151
C	PRO296
C	GLY297
C	ALA330
C	HOH522
C	HOH532
D	PRO291
D	ALA292

site_id	AD3
Number of Residues	2
Details	binding site for residue PO4 C 403

Chain	Residue
C	ARG148
C	HIS258

site_id	AD4
Number of Residues	2
Details	binding site for residue CL C 404

Chain	Residue
C	GLN95
C	HIS171

site_id	AD5
Number of Residues	5
Details	binding site for residue PEG D 401

Chain	Residue
D	HIS210
D	THR312
D	GLU313
D	LYS314
D	HOH580

site_id	AD6
Number of Residues	7
Details	binding site for residue 8E1 D 402

Chain	Residue
D	ASP132
D	PHE134
D	GLY135
D	SER136
D	ASP137
D	VAL196
D	HOH581

site_id	AD7
Number of Residues	2
Details	binding site for residue CL D 403

Chain	Residue
C	ASN294
D	HIS258

site_id	AD8
Number of Residues	1
Details	binding site for residue CL D 404

Chain	Residue
D	ARG89

site_id	AD9
Number of Residues	2
Details	binding site for residue CL D 405

Chain	Residue
D	LYS98
D	HIS171

site_id	AE1
Number of Residues	1
Details	binding site for residue CL D 406

Chain	Residue
D	ARG241

Functional Information from PROSITE/UniProt

site_id	PS00107
Number of Residues	29
Details	PROTEIN_KINASE_ATP Protein kinases ATP-binding region signature. IGQGGFGCIYlAdmnssesvgsdap.....CVVK

Chain	Residue	Details
A	ILE43-LYS71

site_id	PS00108
Number of Residues	13
Details	PROTEIN_KINASE_ST Serine/Threonine protein kinases active-site signature. YvHgDIKasNLLL

Chain	Residue	Details
A	TYR173-LEU185

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Proton acceptor => ECO:0000255\|PROSITE-ProRule:PRU00159, ECO:0000255\|PROSITE-ProRule:PRU10027

Chain	Residue	Details
A	ASP177
B	ASP177
C	ASP177
D	ASP177

site_id	SWS_FT_FI2
Number of Residues	8
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00159

Chain	Residue	Details
A	ILE43
A	LYS71
B	ILE43
B	LYS71
C	ILE43
C	LYS71
D	ILE43
D	LYS71

site_id	SWS_FT_FI3
Number of Residues	4
Details	MOD_RES: Phosphoserine; by PLK3 => ECO:0000269\|PubMed:19103756, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER342
B	SER342
C	SER342
D	SER342

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: Phosphothreonine; by autocatalysis => ECO:0000269\|PubMed:11883897

Chain	Residue	Details
A	THR355
B	THR355
C	THR355
D	THR355

site_id	SWS_FT_FI5
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
A	LYS71
B	LYS71
C	LYS71
D	LYS71

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