Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3FHY

Crystal structure of D235N mutant of 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	5
Details	BINDING SITE FOR RESIDUE MG A 400

Chain	Residue
A	ASP118
A	SO4316
A	HOH320
A	ATP409
A	HOH418

site_id	AC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE NA A 402

Chain	Residue
A	GLU153
A	THR186
A	ATP409
A	HOH419
A	ASP113
A	THR148
A	PRO149
A	ASN150

site_id	AC3
Number of Residues	21
Details	BINDING SITE FOR RESIDUE ATP A 409

Chain	Residue
A	ASP113
A	ASP118
A	ASN150
A	GLU153
A	THR186
A	SER187
A	VAL201
A	ARG224
A	VAL226
A	ALA228
A	THR233
A	GLY234
A	LEU263
A	LEU267
A	SO4316
A	SO4317
A	HOH325
A	MG400
A	NA402
A	HOH417
A	HOH418

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 313

Chain	Residue
A	CYS5
A	LEU31
A	PHE33
A	LYS247

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 A 314

Chain	Residue
A	GLU155
A	LYS161

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 315

Chain	Residue
A	GLY179
A	ASP181
A	MPD318
A	HOH345
A	HOH369

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 A 316

Chain	Residue
A	MG400
A	ATP409

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 317

Chain	Residue
A	GLY232
A	THR233
A	GLY234
A	ASN235
A	ATP409

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD A 318

Chain	Residue
A	ASP181
A	ARG206
A	ARG208
A	SO4315

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD A 319

Chain	Residue
A	GLN63
A	TYR66
A	ARG70
A	MET93
A	ASP96
A	GLU100

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 404

Chain	Residue
B	ASP118
B	SO4318
B	ATP407
B	HOH419
B	HOH422

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA B 406

Chain	Residue
B	ASP113
B	THR148
B	ASN150
B	THR186
B	ATP407
B	HOH418

site_id	BC4
Number of Residues	19
Details	BINDING SITE FOR RESIDUE ATP B 407

Chain	Residue
B	ASP113
B	ASP118
B	ASN150
B	GLU153
B	THR186
B	SER187
B	VAL201
B	ARG224
B	VAL226
B	ALA228
B	THR233
B	GLY234
B	LEU267
B	SO4318
B	SO4319
B	HOH383
B	MG404
B	NA406
B	HOH419

site_id	BC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SO4 B 313

Chain	Residue
B	ARG160

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 314

Chain	Residue
B	CYS5
B	LEU31
B	GLY32
B	HIS246

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 315

Chain	Residue
B	VAL56
B	GLU61
B	HOH357
B	HOH392
A	VAL56
A	GLU61

site_id	BC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 B 316

Chain	Residue
B	ARG70
B	GLU100

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 317

Chain	Residue
B	ASP145
B	GLY179
B	ASP181
B	HOH342
B	HOH360

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 318

Chain	Residue
B	LEU199
B	MG404
B	ATP407

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 319

Chain	Residue
B	VAL231
B	GLY232
B	THR233
B	GLY234
B	ASN235
B	ATP407

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD B 320

Chain	Residue
B	ASP181
B	ARG207
B	ARG208
B	HOH326

site_id	CC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MPD B 321

Chain	Residue
B	ASP173
B	LEU312

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MPD B 322

Chain	Residue
B	HIS248
B	PRO249
B	ASN250
B	ASN251

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MPD B 323

Chain	Residue
B	GLY124
B	GLU130

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD B 324

Chain	Residue
B	VAL19
B	HIS46
B	THR47
B	VAL231
B	HOH403

site_id	CC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MPD B 325

Chain	Residue
B	PRO191
B	PRO193
B	ARG220

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

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