Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1RFU

Crystal structure of pyridoxal kinase complexed with ADP and PLP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0005524	molecular_function	ATP binding
A	0005829	cellular_component	cytosol
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	0042822	biological_process	pyridoxal phosphate metabolic process
A	0046872	molecular_function	metal ion binding
B	0000166	molecular_function	nucleotide binding
B	0005524	molecular_function	ATP binding
B	0005829	cellular_component	cytosol
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	0042822	biological_process	pyridoxal phosphate metabolic process
B	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide binding
C	0005524	molecular_function	ATP binding
C	0005829	cellular_component	cytosol
C	0008478	molecular_function	pyridoxal kinase activity
C	0009443	biological_process	pyridoxal 5'-phosphate salvage
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0042822	biological_process	pyridoxal phosphate metabolic process
C	0046872	molecular_function	metal ion binding
D	0000166	molecular_function	nucleotide binding
D	0005524	molecular_function	ATP binding
D	0005829	cellular_component	cytosol
D	0008478	molecular_function	pyridoxal kinase activity
D	0009443	biological_process	pyridoxal 5'-phosphate salvage
D	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0042822	biological_process	pyridoxal phosphate metabolic process
D	0046872	molecular_function	metal ion binding
E	0000166	molecular_function	nucleotide binding
E	0005524	molecular_function	ATP binding
E	0005829	cellular_component	cytosol
E	0008478	molecular_function	pyridoxal kinase activity
E	0009443	biological_process	pyridoxal 5'-phosphate salvage
E	0016301	molecular_function	kinase activity
E	0016740	molecular_function	transferase activity
E	0042822	biological_process	pyridoxal phosphate metabolic process
E	0046872	molecular_function	metal ion binding
F	0000166	molecular_function	nucleotide binding
F	0005524	molecular_function	ATP binding
F	0005829	cellular_component	cytosol
F	0008478	molecular_function	pyridoxal kinase activity
F	0009443	biological_process	pyridoxal 5'-phosphate salvage
F	0016301	molecular_function	kinase activity
F	0016740	molecular_function	transferase activity
F	0042822	biological_process	pyridoxal phosphate metabolic process
F	0046872	molecular_function	metal ion binding
G	0000166	molecular_function	nucleotide binding
G	0005524	molecular_function	ATP binding
G	0005829	cellular_component	cytosol
G	0008478	molecular_function	pyridoxal kinase activity
G	0009443	biological_process	pyridoxal 5'-phosphate salvage
G	0016301	molecular_function	kinase activity
G	0016740	molecular_function	transferase activity
G	0042822	biological_process	pyridoxal phosphate metabolic process
G	0046872	molecular_function	metal ion binding
H	0000166	molecular_function	nucleotide binding
H	0005524	molecular_function	ATP binding
H	0005829	cellular_component	cytosol
H	0008478	molecular_function	pyridoxal kinase activity
H	0009443	biological_process	pyridoxal 5'-phosphate salvage
H	0016301	molecular_function	kinase activity
H	0016740	molecular_function	transferase activity
H	0042822	biological_process	pyridoxal phosphate metabolic process
H	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN A 403

Chain	Residue
A	TYR127
A	PLP401
A	ADP402

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN B 1403

Chain	Residue
B	VAL115
B	PLP1401
B	ADP1402

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN C 2403

Chain	Residue
C	VAL115
C	PLP2401
C	ADP2402

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 3403

Chain	Residue
D	ASP113
D	VAL115
D	PLP3401
D	ADP3402

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 4403

Chain	Residue
E	ASP113
E	VAL115
E	PLP4401
E	ADP4402

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 5403

Chain	Residue
F	ASP113
F	VAL115
F	PLP5401
F	ADP5402

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN G 6403

Chain	Residue
G	ASP113
G	PLP6401
G	ADP6402

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 7403

Chain	Residue
H	ASP113
H	VAL115
H	PLP7401
H	ADP7402

site_id	AC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PLP A 401

Chain	Residue
A	SER12
A	VAL19
A	THR47
A	TYR84
A	TYR127
A	VAL231
A	GLY232
A	THR233
A	GLY234
A	ASP235
A	ADP402
A	ZN403

site_id	BC1
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ADP A 402

Chain	Residue
A	ASN150
A	THR186
A	SER187
A	LEU199
A	MET223
A	HIS224
A	LYS225
A	VAL226
A	ALA228
A	THR233
A	GLY234
A	PHE237
A	MET263
A	LEU267
A	PLP401
A	ZN403

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PLP B 1401

Chain	Residue
B	SER12
B	VAL19
B	THR47
B	TYR84
B	TYR127
B	VAL231
B	GLY232
B	THR233
B	GLY234
B	ASP235
B	ADP1402
B	ZN1403

site_id	BC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ADP B 1402

Chain	Residue
B	THR186
B	SER187
B	MET223
B	HIS224
B	LYS225
B	VAL226
B	ALA228
B	THR233
B	GLY234
B	MET263
B	LEU267
B	PLP1401
B	ZN1403

site_id	BC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PLP C 2401

Chain	Residue
C	SER12
C	VAL19
C	THR47
C	TYR84
C	TYR127
C	VAL231
C	GLY232
C	THR233
C	GLY234
C	ASP235
C	ADP2402
C	ZN2403

site_id	BC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ADP C 2402

Chain	Residue
C	LYS225
C	VAL226
C	ALA228
C	THR233
C	GLY234
C	MET263
C	LEU267
C	PLP2401
C	ZN2403
C	ASN150
C	THR186
C	SER187
C	LEU199
C	MET223
C	HIS224

site_id	BC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PLP D 3401

Chain	Residue
D	SER12
D	VAL19
D	THR47
D	TYR84
D	TYR127
D	VAL231
D	GLY232
D	THR233
D	GLY234
D	ASP235
D	ADP3402
D	ZN3403

site_id	BC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ADP D 3402

Chain	Residue
D	ASN150
D	THR186
D	SER187
D	LEU199
D	MET223
D	HIS224
D	LYS225
D	VAL226
D	ALA228
D	THR233
D	GLY234
D	MET263
D	LEU267
D	PLP3401
D	ZN3403

site_id	BC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PLP E 4401

Chain	Residue
E	SER12
E	VAL19
E	THR47
E	TYR84
E	TYR127
E	VAL231
E	GLY232
E	THR233
E	GLY234
E	ASP235
E	ADP4402
E	ZN4403

site_id	BC9
Number of Residues	14
Details	BINDING SITE FOR RESIDUE ADP E 4402

Chain	Residue
E	ASN150
E	THR186
E	SER187
E	MET223
E	HIS224
E	LYS225
E	VAL226
E	ALA228
E	THR233
E	GLY234
E	MET263
E	LEU267
E	PLP4401
E	ZN4403

site_id	CC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PLP F 5401

Chain	Residue
F	SER12
F	VAL19
F	THR47
F	TYR84
F	TYR127
F	VAL231
F	GLY232
F	GLY234
F	ASP235
F	ADP5402
F	ZN5403

site_id	CC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE ADP F 5402

Chain	Residue
F	ASN150
F	THR186
F	SER187
F	MET223
F	HIS224
F	LYS225
F	VAL226
F	ALA228
F	THR233
F	GLY234
F	MET263
F	LEU267
F	PLP5401
F	ZN5403

site_id	CC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PLP G 6401

Chain	Residue
G	SER12
G	VAL19
G	THR47
G	TYR84
G	TYR127
G	VAL231
G	GLY232
G	GLY234
G	ASP235
G	ADP6402
G	ZN6403

site_id	CC4
Number of Residues	14
Details	BINDING SITE FOR RESIDUE ADP G 6402

Chain	Residue
G	ASN150
G	THR186
G	SER187
G	MET223
G	HIS224
G	LYS225
G	VAL226
G	ALA228
G	THR233
G	GLY234
G	MET263
G	LEU267
G	PLP6401
G	ZN6403

site_id	CC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PLP H 7401

Chain	Residue
H	SER12
H	VAL19
H	THR47
H	TYR84
H	TYR127
H	VAL231
H	GLY232
H	THR233
H	GLY234
H	ASP235
H	ADP7402
H	ZN7403

site_id	CC6
Number of Residues	14
Details	BINDING SITE FOR RESIDUE ADP H 7402

Chain	Residue
H	ASN150
H	THR186
H	SER187
H	MET223
H	HIS224
H	LYS225
H	VAL226
H	ALA228
H	THR233
H	GLY234
H	MET263
H	LEU267
H	PLP7401
H	ZN7403

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"O00764","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14722069","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1RFT","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12235162","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14722069","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LHR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1RFT","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	32
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14722069","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1RFU","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12235162","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14722069","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LHR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	40
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12235162","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LHR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	8
Details	Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"PubMed","id":"10395444","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	32
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"O00764","evidenceCode":"ECO:0000250"}]}

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

site_id	CSA3
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
C	GLY234
C	THR233
C	GLY232
C	ASP235

site_id	CSA4
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
D	GLY234
D	THR233
D	GLY232
D	ASP235

site_id	CSA5
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
E	GLY234
E	THR233
E	GLY232
E	ASP235

site_id	CSA6
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
F	GLY234
F	THR233
F	GLY232
F	ASP235

site_id	CSA7
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
G	GLY234
G	THR233
G	GLY232
G	ASP235

site_id	CSA8
Number of Residues	4
Details	Annotated By Reference To The Literature 1tz3

Chain	Residue	Details
H	GLY234
H	THR233
H	GLY232
H	ASP235

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