Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4EN4

Crystal Structure of the Ternary Human PL Kinase-Ginkgotoxin-MgATP Complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000287	molecular_function	magnesium ion binding
A	0005524	molecular_function	ATP binding
A	0005576	cellular_component	extracellular region
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005829	cellular_component	cytosol
A	0008270	molecular_function	zinc ion binding
A	0008478	molecular_function	pyridoxal kinase activity
A	0009443	biological_process	pyridoxal 5'-phosphate salvage
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
A	0030170	molecular_function	pyridoxal phosphate binding
A	0030955	molecular_function	potassium ion binding
A	0031402	molecular_function	sodium ion binding
A	0031403	molecular_function	lithium ion binding
A	0034774	cellular_component	secretory granule lumen
A	0035580	cellular_component	specific granule lumen
A	0042803	molecular_function	protein homodimerization activity
A	0042816	biological_process	vitamin B6 metabolic process
A	0042822	biological_process	pyridoxal phosphate metabolic process
A	0046872	molecular_function	metal ion binding
A	0070062	cellular_component	extracellular exosome
B	0000166	molecular_function	nucleotide binding
B	0000287	molecular_function	magnesium ion binding
B	0005524	molecular_function	ATP binding
B	0005576	cellular_component	extracellular region
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005829	cellular_component	cytosol
B	0008270	molecular_function	zinc ion binding
B	0008478	molecular_function	pyridoxal kinase activity
B	0009443	biological_process	pyridoxal 5'-phosphate salvage
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
B	0030170	molecular_function	pyridoxal phosphate binding
B	0030955	molecular_function	potassium ion binding
B	0031402	molecular_function	sodium ion binding
B	0031403	molecular_function	lithium ion binding
B	0034774	cellular_component	secretory granule lumen
B	0035580	cellular_component	specific granule lumen
B	0042803	molecular_function	protein homodimerization activity
B	0042816	biological_process	vitamin B6 metabolic process
B	0042822	biological_process	pyridoxal phosphate metabolic process
B	0046872	molecular_function	metal ion binding
B	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 401

Chain	Residue
A	ASP118
A	ATP404
A	MPD406
A	HOH589
A	HOH590

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE NA A 402

Chain	Residue
A	THR186
A	ATP404
A	HOH518
A	ASP113
A	THR148
A	PRO149
A	ASN150

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 403

Chain	Residue
A	ASP235
A	ATP404
A	GT0405
A	GT1410

site_id	AC4
Number of Residues	24
Details	BINDING SITE FOR RESIDUE ATP A 404

Chain	Residue
A	ASP113
A	ASP118
A	ASN150
A	GLU153
A	THR186
A	SER187
A	VAL201
A	ARG224
A	LYS225
A	VAL226
A	ALA228
A	THR233
A	GLY234
A	PHE237
A	LEU267
A	MG401
A	NA402
A	MG403
A	MPD406
A	GT1410
A	HOH509
A	HOH515
A	HOH595
A	HOH596

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GT0 A 405

Chain	Residue
A	SER12
A	GLY20
A	HIS46
A	THR47
A	TYR84
A	VAL231
A	ASP235
A	MG403
A	HOH501

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MPD A 406

Chain	Residue
A	ASP118
A	TRP120
A	LEU199
A	MG401
A	ATP404
A	HOH589
A	HOH590
A	HOH594

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 407

Chain	Residue
A	GLN63
A	ARG70
A	MET93
A	GLU100

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 A 408

Chain	Residue
A	GLY159
A	LYS161

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 409

Chain	Residue
A	LEU31
A	GLY32
A	HIS246
A	LYS247

site_id	BC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GT1 A 410

Chain	Residue
A	SER12
A	THR47
A	TYR84
A	VAL231
A	GLY232
A	THR233
A	GLY234
A	ASP235
A	MG403
A	ATP404
A	HOH590

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 401

Chain	Residue
B	ASP118
B	ATP404
B	MPD407
B	HOH505
B	HOH506

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA B 402

Chain	Residue
B	ASP113
B	THR148
B	PRO149
B	THR186
B	ATP404
B	HOH507

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 403

Chain	Residue
B	VAL115
B	ASP235
B	ATP404
B	GT1405
B	GT0414

site_id	BC5
Number of Residues	26
Details	BINDING SITE FOR RESIDUE ATP B 404

Chain	Residue
B	SER187
B	LEU199
B	VAL201
B	ARG224
B	LYS225
B	VAL226
B	ALA228
B	THR233
B	GLY234
B	LEU263
B	LEU267
B	MG401
B	NA402
B	MG403
B	GT1405
B	MPD407
B	HOH506
B	HOH546
B	HOH576
B	HOH577
B	HOH626
B	ASP113
B	ASP118
B	ASN150
B	GLU153
B	THR186

site_id	BC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GT1 B 405

Chain	Residue
B	SER12
B	THR47
B	TYR84
B	VAL231
B	GLY232
B	THR233
B	GLY234
B	ASP235
B	MG403
B	ATP404
B	HOH506

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD B 406

Chain	Residue
B	ASP181
B	ARG207
B	ARG208
B	MPD410

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD B 407

Chain	Residue
B	ASP118
B	MG401
B	ATP404
B	HOH505
B	HOH547
B	HOH605

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD B 408

Chain	Residue
B	ASP173
B	SER177
B	ARG206
B	LEU312
B	HOH633

site_id	CC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MPD B 409

Chain	Residue
B	GLN165
B	PRO193

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD B 410

Chain	Residue
B	GLY179
B	ASP181
B	MPD406
B	HOH528
B	HOH529
B	HOH602

site_id	CC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SO4 B 411

Chain	Residue
B	GLY159

site_id	CC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 B 412

Chain	Residue
B	ARG70
B	GLU100

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 413

Chain	Residue
B	LEU31
B	GLY32
B	LYS247

site_id	CC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GT0 B 414

Chain	Residue
B	SER12
B	VAL19
B	PHE43
B	HIS46
B	THR47
B	VAL231
B	ASP235
B	MG403

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"17766369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"17766369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"2YXT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3FHY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"17766369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"2YXU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3FHY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22879864","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EN4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19351586","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme.","authors":["Gandhi A.K.","Musayev F.N.","Safo M.K."]}},{"source":"PDB","id":"3FHX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3KEU","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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