Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2AJP

Crystal structure of a 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	2
Details	BINDING SITE FOR RESIDUE MG A 401

Chain	Residue
A	ASP118
A	ANP501

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG B 1401

Chain	Residue
B	ASP118
B	ANP1501

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX A 402

Chain	Residue
A	GLY232
A	THR233
A	GLY234
A	ANP501

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX A 403

Chain	Residue
A	GLU34
A	ASP36
B	ARG16
A	ARG6

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNX B 404

Chain	Residue
A	ASP36
B	ARG16
B	GLY17
B	TYR18
B	ARG22

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX A 405

Chain	Residue
A	THR82
A	GLY83
A	ASP113
A	TYR136

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE UNX A 406

Chain	Residue
A	VAL14
A	ARG16
A	GLY17
A	ASN45
A	HIS46
A	GLU290

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE UNX A 407

Chain	Residue
A	HIS264
A	GLN268

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX A 408

Chain	Residue
A	GLN11
A	GLY83
A	TYR84
A	ASP235

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNX B 409

Chain	Residue
A	TYR18
A	VAL294
B	GLN29
B	PHE33
B	ILE35

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX A 410

Chain	Residue
A	ARG22
A	THR25
A	PHE26
B	GLN29

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNX B 411

Chain	Residue
A	GLN29
A	VAL30
A	GLY32
B	VAL294
B	LYS297

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE UNX B 412

Chain	Residue
A	ASP36
A	ALA37
B	HIS13
B	VAL14
B	ILE15
B	ARG22

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE UNX A 413

Chain	Residue
A	ASN75
A	LYS76
A	TYR77
A	LEU101
A	ASN105
A	LEU108

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UNX A 414

Chain	Residue
A	PRO142
A	ALA144
A	GLY179

site_id	BC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE UNX A 415

Chain	Residue
A	GLN165

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX A 416

Chain	Residue
A	HIS46
A	PRO286
A	LEU289
A	GLU290

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX A 417

Chain	Residue
A	TYR18
A	VAL231
A	GLU290
A	LEU291

site_id	CC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE UNX A 418

Chain	Residue
A	PRO249
A	ASN250

site_id	CC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE UNX A 419

Chain	Residue
A	LEU199
A	LYS225

site_id	CC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE UNX A 420

Chain	Residue
A	PHE33
A	HIS246

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNX A 421

Chain	Residue
A	ASP113
A	THR148
A	THR186
A	GLY234
A	ANP501

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNX B 1402

Chain	Residue
B	GLY232
B	THR233
B	GLY234
B	ASP235
B	ANP1501

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UNX B 1403

Chain	Residue
B	ARG6
B	GLU34
B	ASP36

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX A 1404

Chain	Residue
A	GLY17
A	TYR18
A	ARG22
B	ASP36

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNX B 1405

Chain	Residue
B	THR82
B	GLY83
B	CYS112
B	ASP113
B	TYR136

site_id	CC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE UNX B 1406

Chain	Residue
B	VAL14
B	ARG16
B	GLY17
B	ASN45
B	HIS46
B	GLU290

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX B 1408

Chain	Residue
B	GLN11
B	GLY83
B	TYR84
B	ASP235

site_id	DC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNX A 1409

Chain	Residue
A	GLN29
A	ILE35
B	TYR18
B	ARG22
B	VAL294

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX B 1410

Chain	Residue
B	ASN21
B	ARG22
B	THR25
B	PHE26

site_id	DC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNX A 1411

Chain	Residue
A	VAL294
A	LYS297
B	GLN29
B	VAL30

site_id	DC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE UNX A 1412

Chain	Residue
A	HIS13
A	VAL14
A	ILE15
A	ARG22
B	ASP36
B	ALA37

site_id	DC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE UNX B 1413

Chain	Residue
B	ASN75
B	LYS76
B	TYR77
B	LEU101
B	ASN105
B	LEU108

site_id	DC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UNX B 1414

Chain	Residue
B	PRO142
B	ALA144
B	ASP145

site_id	DC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UNX B 1415

Chain	Residue
B	SER164
B	GLN165
B	PRO191

site_id	DC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UNX B 1416

Chain	Residue
B	VAL231
B	LEU289
B	UNX1417

site_id	EC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UNX B 1417

Chain	Residue
B	TYR18
B	VAL231
B	GLU290
B	LEU291
B	UNX1416

site_id	EC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UNX B 1418

Chain	Residue
B	HIS248
B	PRO249
B	ASN250

site_id	EC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE UNX B 1419

Chain	Residue
B	LEU199

site_id	EC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UNX B 1420

Chain	Residue
B	LEU31
B	PHE33
B	LYS247

site_id	EC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UNX B 1421

Chain	Residue
B	THR148
B	THR186
B	ANP1501

site_id	EC6
Number of Residues	17
Details	BINDING SITE FOR RESIDUE ANP A 501

Chain	Residue
A	ASP113
A	ASP118
A	ASN150
A	GLU153
A	THR186
A	SER187
A	VAL201
A	VAL226
A	ALA228
A	PHE230
A	THR233
A	GLY234
A	PHE237
A	LEU267
A	MG401
A	UNX402
A	UNX421

site_id	EC7
Number of Residues	17
Details	BINDING SITE FOR RESIDUE ANP B 1501

Chain	Residue
B	ASP113
B	VAL115
B	ASP118
B	ASN150
B	GLU153
B	THR186
B	SER187
B	LEU199
B	VAL201
B	LYS225
B	VAL226
B	ALA228
B	PHE230
B	THR233
B	MG1401
B	UNX1402
B	UNX1421

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"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19369195","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)