Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6AC9

Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000785	cellular_component	chromatin
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	0007077	biological_process	mitotic nuclear membrane disassembly
A	0007165	biological_process	signal transduction
A	0015030	cellular_component	Cajal body
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0019901	molecular_function	protein kinase binding
A	0030576	biological_process	Cajal body organization
A	0031175	biological_process	neuron projection development
A	0031492	molecular_function	nucleosomal DNA binding
A	0035175	molecular_function	histone H3S10 kinase activity
A	0042393	molecular_function	histone binding
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
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
A	0141003	molecular_function	histone H2AX kinase activity
A	2001222	biological_process	regulation of neuron migration
B	0000166	molecular_function	nucleotide binding
B	0000785	cellular_component	chromatin
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	0007077	biological_process	mitotic nuclear membrane disassembly
B	0007165	biological_process	signal transduction
B	0015030	cellular_component	Cajal body
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0019901	molecular_function	protein kinase binding
B	0030576	biological_process	Cajal body organization
B	0031175	biological_process	neuron projection development
B	0031492	molecular_function	nucleosomal DNA binding
B	0035175	molecular_function	histone H3S10 kinase activity
B	0042393	molecular_function	histone binding
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
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
B	0141003	molecular_function	histone H2AX kinase activity
B	2001222	biological_process	regulation of neuron migration
C	0000166	molecular_function	nucleotide binding
C	0000785	cellular_component	chromatin
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	0007077	biological_process	mitotic nuclear membrane disassembly
C	0007165	biological_process	signal transduction
C	0015030	cellular_component	Cajal body
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0019901	molecular_function	protein kinase binding
C	0030576	biological_process	Cajal body organization
C	0031175	biological_process	neuron projection development
C	0031492	molecular_function	nucleosomal DNA binding
C	0035175	molecular_function	histone H3S10 kinase activity
C	0042393	molecular_function	histone binding
C	0045944	biological_process	positive regulation of transcription by RNA polymerase II
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
C	0141003	molecular_function	histone H2AX kinase activity
C	2001222	biological_process	regulation of neuron migration
D	0000166	molecular_function	nucleotide binding
D	0000785	cellular_component	chromatin
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	0007077	biological_process	mitotic nuclear membrane disassembly
D	0007165	biological_process	signal transduction
D	0015030	cellular_component	Cajal body
D	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0019901	molecular_function	protein kinase binding
D	0030576	biological_process	Cajal body organization
D	0031175	biological_process	neuron projection development
D	0031492	molecular_function	nucleosomal DNA binding
D	0035175	molecular_function	histone H3S10 kinase activity
D	0042393	molecular_function	histone binding
D	0045944	biological_process	positive regulation of transcription by RNA polymerase II
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
D	0141003	molecular_function	histone H2AX kinase activity
D	2001222	biological_process	regulation of neuron migration

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	binding site for residue ANP A 401

Chain	Residue
A	ILE51
A	MG402
A	HOH586
A	VAL69
A	LYS71
A	MET131
A	ASP132
A	ARG133
A	PHE134
A	LEU184
A	ASP197

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

Chain	Residue
A	ASP197
A	ANP401
A	HOH586
A	HOH670

site_id	AC3
Number of Residues	3
Details	binding site for residue SO4 A 403

Chain	Residue
A	GLN95
A	HIS171
A	HOH512

site_id	AC4
Number of Residues	6
Details	binding site for residue SO4 A 404

Chain	Residue
A	ASP120
A	LYS121
A	ASN122
A	HOH535
A	HOH598
D	ARG89

site_id	AC5
Number of Residues	2
Details	binding site for residue CL A 405

Chain	Residue
A	ARG148
A	HIS258

site_id	AC6
Number of Residues	12
Details	binding site for residue PG4 A 406

Chain	Residue
A	PHE81
A	LYS85
A	ARG89
A	ARG203
A	PRO206
A	LYS211
A	HOH702
D	ARG279
D	LYS307
D	LEU308
D	LEU309
D	GOL403

site_id	AC7
Number of Residues	10
Details	binding site for residue ANP B 401

Chain	Residue
B	ILE51
B	VAL69
B	MET131
B	ASP132
B	PHE134
B	LEU184
B	ASP197
B	MG406
B	HOH579
B	HOH646

site_id	AC8
Number of Residues	2
Details	binding site for residue CL B 402

Chain	Residue
B	ARG148
B	HIS258

site_id	AC9
Number of Residues	6
Details	binding site for residue SO4 B 403

Chain	Residue
B	ARG89
B	ARG203
B	HOH568
B	HOH601
B	HOH654
C	GOL401

site_id	AD1
Number of Residues	3
Details	binding site for residue SO4 B 404

Chain	Residue
B	GLN95
B	HIS171
B	HOH638

site_id	AD2
Number of Residues	7
Details	binding site for residue SO4 B 405

Chain	Residue
B	ARG151
B	GLY297
B	HOH536
B	HOH541
D	PRO291
D	ALA292
D	HOH582

site_id	AD3
Number of Residues	4
Details	binding site for residue MG B 406

Chain	Residue
B	ASP197
B	ANP401
B	HOH579
B	HOH652

site_id	AD4
Number of Residues	9
Details	binding site for residue PG4 B 407

Chain	Residue
B	TYR213
B	ARG241
B	ARG279
B	LYS307
B	LEU309
B	ASP310
B	TYR311
B	THR312
B	HOH526

site_id	AD5
Number of Residues	7
Details	binding site for residue GOL C 401

Chain	Residue
B	ARG89
B	SO4403
B	HOH568
C	ARG241
C	ASP310
C	HOH556
C	HOH581

site_id	AD6
Number of Residues	12
Details	binding site for residue ANP C 402

Chain	Residue
C	ILE51
C	VAL69
C	LYS71
C	MET131
C	ASP132
C	PHE134
C	ASN182
C	LEU184
C	ASP197
C	MG405
C	HOH539
C	HOH551

site_id	AD7
Number of Residues	2
Details	binding site for residue SO4 C 403

Chain	Residue
C	HIS171
C	GLN95

site_id	AD8
Number of Residues	2
Details	binding site for residue CL C 404

Chain	Residue
C	ARG148
C	HIS258

site_id	AD9
Number of Residues	5
Details	binding site for residue MG C 405

Chain	Residue
C	LYS71
C	ASP197
C	ANP402
C	HOH539
C	HOH551

site_id	AE1
Number of Residues	4
Details	binding site for residue MG D 401

Chain	Residue
D	ASN182
D	ASP197
D	ANP402
D	HOH588

site_id	AE2
Number of Residues	16
Details	binding site for residue ANP D 402

Chain	Residue
D	ILE51
D	VAL69
D	LYS71
D	MET131
D	ASP132
D	ARG133
D	PHE134
D	ASP137
D	SER181
D	ASN182
D	LEU184
D	ASP197
D	MG401
D	HOH510
D	HOH588
D	HOH633

site_id	AE3
Number of Residues	6
Details	binding site for residue GOL D 403

Chain	Residue
A	ARG89
A	PG4406
A	HOH559
D	ARG241
D	HOH586
D	HOH593

site_id	AE4
Number of Residues	3
Details	binding site for residue SO4 D 404

Chain	Residue
D	GLN95
D	HIS171
D	HOH545

site_id	AE5
Number of Residues	2
Details	binding site for residue CL D 405

Chain	Residue
D	ARG148
D	HIS258

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)