Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2YXU

Human Pyridoxal Kinase

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	3
Details	BINDING SITE FOR RESIDUE MG A 1404

Chain	Residue
A	ASP118
A	HOH1506
A	HOH1507

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA A 1406

Chain	Residue
A	ASP113
A	THR148
A	THR186
A	HOH1508

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG B 2404

Chain	Residue
B	HOH2412
B	ASP118
B	HOH2411

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA B 2406

Chain	Residue
B	THR148
B	THR186
B	HOH2413

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PO4 A 1501

Chain	Residue
A	CYS5
A	LEU31
A	GLY32

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PO4 B 1517

Chain	Residue
B	LEU31
B	GLY32
B	HIS246

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 B 1527

Chain	Residue
B	GLN63
B	GLU100

site_id	AC8
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ATP A 1410

Chain	Residue
A	ASP113
A	ASP118
A	TYR127
A	ASN150
A	GLU153
A	THR186
A	SER187
A	ARG224
A	LYS225
A	ALA228
A	THR233
A	GLY234
A	LEU267
A	HOH1506
A	HOH1507
A	HOH1510

site_id	AC9
Number of Residues	21
Details	BINDING SITE FOR RESIDUE ATP B 2410

Chain	Residue
B	ASP113
B	ASP118
B	TYR127
B	THR148
B	ASN150
B	GLU153
B	THR186
B	SER187
B	LEU199
B	ARG224
B	LYS225
B	ALA228
B	THR233
B	GLY234
B	LEU263
B	LEU267
B	HOH2411
B	HOH2412
B	HOH2419
B	HOH2500
B	HOH2540

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD A 1011

Chain	Residue
A	TYR66
A	ARG70
A	MET93
A	GLU100

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD A 1013

Chain	Residue
A	SER12
A	HIS46
A	THR47
A	TYR84
A	HOH1602

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MPD B 1015

Chain	Residue
B	PRO142
B	ALA144
B	ASP145
B	GLY179
B	PRO180
B	ASP181
B	HOH2438
B	HOH2466

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD B 1019

Chain	Residue
B	SER12
B	HIS46
B	THR47
B	ASP235
B	HOH2600

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MPD B 1021

Chain	Residue
B	ASP181
B	ARG208

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MPD B 1023

Chain	Residue
B	SER177
B	ARG206
B	LEU312

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD B 1025

Chain	Residue
B	HIS248
B	PRO249
B	ASN250
B	ASN251
B	HOH2546

site_id	BC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MPD B 1029

Chain	Residue
B	GLU123
B	GLY124

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD B 1031

Chain	Residue
A	PRO191
B	PHE43
B	TYR84
B	ARG86

site_id	CC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MPD A 1037

Chain	Residue
A	ASP118
A	HOH1507

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD B 1039

Chain	Residue
B	HOH2412
B	HOH2485
B	HOH2500
B	ASP118

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MPD B 1041

Chain	Residue
B	PRO191
B	HOH2441
B	HOH2443

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

Catalytic Information from CSA

site_id	CSA1
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
A	GLY234
A	THR233
A	GLY232
A	ASP235

site_id	CSA2
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
B	GLY234
B	THR233
B	GLY232
B	ASP235

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