Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6YJZ

Crystal structure of mouse pyridoxal kinase in apo form

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0005524	molecular_function	ATP binding
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0008270	molecular_function	zinc ion binding
A	0008478	molecular_function	pyridoxal kinase activity
A	0008614	biological_process	pyridoxine metabolic process
A	0009443	biological_process	pyridoxal 5'-phosphate salvage
A	0016301	molecular_function	kinase 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	0036094	molecular_function	small molecule binding
A	0042803	molecular_function	protein homodimerization activity
A	0042816	biological_process	vitamin B6 metabolic process
A	0042817	biological_process	pyridoxal metabolic process
A	0042818	biological_process	pyridoxamine metabolic process
A	0042822	biological_process	pyridoxal phosphate metabolic process
A	0042823	biological_process	pyridoxal phosphate biosynthetic process
A	0043066	biological_process	negative regulation of apoptotic process
A	0046872	molecular_function	metal ion binding
A	0070280	molecular_function	pyridoxal binding
A	0097159	molecular_function	organic cyclic compound binding
B	0000287	molecular_function	magnesium ion binding
B	0005524	molecular_function	ATP binding
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0008270	molecular_function	zinc ion binding
B	0008478	molecular_function	pyridoxal kinase activity
B	0008614	biological_process	pyridoxine metabolic process
B	0009443	biological_process	pyridoxal 5'-phosphate salvage
B	0016301	molecular_function	kinase 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	0036094	molecular_function	small molecule binding
B	0042803	molecular_function	protein homodimerization activity
B	0042816	biological_process	vitamin B6 metabolic process
B	0042817	biological_process	pyridoxal metabolic process
B	0042818	biological_process	pyridoxamine metabolic process
B	0042822	biological_process	pyridoxal phosphate metabolic process
B	0042823	biological_process	pyridoxal phosphate biosynthetic process
B	0043066	biological_process	negative regulation of apoptotic process
B	0046872	molecular_function	metal ion binding
B	0070280	molecular_function	pyridoxal binding
B	0097159	molecular_function	organic cyclic compound binding
C	0000287	molecular_function	magnesium ion binding
C	0005524	molecular_function	ATP binding
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0008270	molecular_function	zinc ion binding
C	0008478	molecular_function	pyridoxal kinase activity
C	0008614	biological_process	pyridoxine metabolic process
C	0009443	biological_process	pyridoxal 5'-phosphate salvage
C	0016301	molecular_function	kinase activity
C	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
C	0030170	molecular_function	pyridoxal phosphate binding
C	0030955	molecular_function	potassium ion binding
C	0031402	molecular_function	sodium ion binding
C	0031403	molecular_function	lithium ion binding
C	0036094	molecular_function	small molecule binding
C	0042803	molecular_function	protein homodimerization activity
C	0042816	biological_process	vitamin B6 metabolic process
C	0042817	biological_process	pyridoxal metabolic process
C	0042818	biological_process	pyridoxamine metabolic process
C	0042822	biological_process	pyridoxal phosphate metabolic process
C	0042823	biological_process	pyridoxal phosphate biosynthetic process
C	0043066	biological_process	negative regulation of apoptotic process
C	0046872	molecular_function	metal ion binding
C	0070280	molecular_function	pyridoxal binding
C	0097159	molecular_function	organic cyclic compound binding
D	0000287	molecular_function	magnesium ion binding
D	0005524	molecular_function	ATP binding
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0008270	molecular_function	zinc ion binding
D	0008478	molecular_function	pyridoxal kinase activity
D	0008614	biological_process	pyridoxine metabolic process
D	0009443	biological_process	pyridoxal 5'-phosphate salvage
D	0016301	molecular_function	kinase activity
D	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
D	0030170	molecular_function	pyridoxal phosphate binding
D	0030955	molecular_function	potassium ion binding
D	0031402	molecular_function	sodium ion binding
D	0031403	molecular_function	lithium ion binding
D	0036094	molecular_function	small molecule binding
D	0042803	molecular_function	protein homodimerization activity
D	0042816	biological_process	vitamin B6 metabolic process
D	0042817	biological_process	pyridoxal metabolic process
D	0042818	biological_process	pyridoxamine metabolic process
D	0042822	biological_process	pyridoxal phosphate metabolic process
D	0042823	biological_process	pyridoxal phosphate biosynthetic process
D	0043066	biological_process	negative regulation of apoptotic process
D	0046872	molecular_function	metal ion binding
D	0070280	molecular_function	pyridoxal binding
D	0097159	molecular_function	organic cyclic compound binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue PG4 A 401

Chain	Residue
A	TRP52
A	TYR84
A	ARG86
A	HOH528
B	VAL306

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

Chain	Residue
A	CYS5
A	LEU31
A	GLY32
A	HIS246

site_id	AC3
Number of Residues	6
Details	binding site for residue EDO A 404

Chain	Residue
A	ASP113
A	TYR127
A	THR148
A	ASN150
A	GLU153
A	THR186

site_id	AC4
Number of Residues	5
Details	binding site for residue PG4 A 405

Chain	Residue
A	THR186
A	VAL226
A	THR233
A	GLY234
A	GLN264

site_id	AC5
Number of Residues	8
Details	binding site for residue GOL A 406

Chain	Residue
A	GLN55
A	VAL56
A	LYS58
A	GLU61
A	HOH545
B	LYS58
B	GLU61
B	GLN194

site_id	AC6
Number of Residues	4
Details	binding site for residue EDO A 407

Chain	Residue
A	TYR66
A	GLU67
A	LYS70
A	GLU100

site_id	AC7
Number of Residues	5
Details	binding site for residue EDO A 408

Chain	Residue
A	ASN39
A	VAL41
A	GLN42
B	ASN39
B	GLN42

site_id	AC8
Number of Residues	1
Details	binding site for residue EDO B 501

Chain	Residue
B	ARG6

site_id	AC9
Number of Residues	5
Details	binding site for residue GOL B 502

Chain	Residue
B	GLU4
B	LEU31
B	GLY32
B	PHE33
B	HIS246

site_id	AD1
Number of Residues	5
Details	binding site for residue EDO B 503

Chain	Residue
B	ASP113
B	THR148
B	ASN150
B	GLU153
B	THR186

site_id	AD2
Number of Residues	2
Details	binding site for residue EDO B 504

Chain	Residue
B	HIS63
B	GLU100

site_id	AD3
Number of Residues	4
Details	binding site for residue EDO B 505

Chain	Residue
B	SER12
B	HIS46
B	THR47
B	TYR84

site_id	AD4
Number of Residues	4
Details	binding site for residue GOL C 701

Chain	Residue
C	GLU4
C	LEU31
C	PHE33
C	HIS246

site_id	AD5
Number of Residues	1
Details	binding site for residue EDO C 702

Chain	Residue
C	LYS119

site_id	AD6
Number of Residues	3
Details	binding site for residue EDO C 703

Chain	Residue
C	GLU155
C	GLY159
C	LYS161

site_id	AD7
Number of Residues	2
Details	binding site for residue EDO C 704

Chain	Residue
C	PHE43
C	THR47

site_id	AD8
Number of Residues	5
Details	binding site for residue EDO C 705

Chain	Residue
C	SER40
C	VAL56
C	LEU57
C	THR85
C	PHE90

site_id	AD9
Number of Residues	4
Details	binding site for residue EDO C 706

Chain	Residue
C	HIS63
C	TYR66
C	GLU67
C	GLU100

site_id	AE1
Number of Residues	5
Details	binding site for residue GOL D 401

Chain	Residue
D	GLU4
D	CYS5
D	LEU31
D	GLY32
D	HIS246

site_id	AE2
Number of Residues	3
Details	binding site for residue EDO D 402

Chain	Residue
D	ARG6
D	LYS76
D	ASP78

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Proton acceptor => ECO:0000250\|UniProtKB:O00764

Chain	Residue	Details
A	ASP235
B	ASP235
C	ASP235
D	ASP235

site_id	SWS_FT_FI2
Number of Residues	40
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:O00764

Chain	Residue	Details
A	SER12
A	GLY234
B	SER12
B	THR47
B	ASP113
B	ASP118
B	THR148
B	ASN150
B	THR186
B	VAL226
B	THR233
A	THR47
B	GLY234
C	SER12
C	THR47
C	ASP113
C	ASP118
C	THR148
C	ASN150
C	THR186
C	VAL226
C	THR233
A	ASP113
C	GLY234
D	SER12
D	THR47
D	ASP113
D	ASP118
D	THR148
D	ASN150
D	THR186
D	VAL226
D	THR233
A	ASP118
D	GLY234
A	THR148
A	ASN150
A	THR186
A	VAL226
A	THR233

site_id	SWS_FT_FI3
Number of Residues	4
Details	MOD_RES: N-acetylmethionine => ECO:0000250\|UniProtKB:P82197

Chain	Residue	Details
A	MET1
B	MET1
C	MET1
D	MET1

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:21183079

Chain	Residue	Details
A	SER59
B	SER59
C	SER59
D	SER59

site_id	SWS_FT_FI5
Number of Residues	12
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:O00764

Chain	Residue	Details
A	SER164
D	SER164
D	SER213
D	SER285
A	SER213
A	SER285
B	SER164
B	SER213
B	SER285
C	SER164
C	SER213
C	SER285

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