Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3F4N

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0008615	biological_process	pyridoxine biosynthetic process
A	0016740	molecular_function	transferase activity
A	0016769	molecular_function	transferase activity, transferring nitrogenous groups
A	0033856	molecular_function	pyridoxine 5'-phosphate synthase activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0008615	biological_process	pyridoxine biosynthetic process
B	0016740	molecular_function	transferase activity
B	0016769	molecular_function	transferase activity, transferring nitrogenous groups
B	0033856	molecular_function	pyridoxine 5'-phosphate synthase activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0008615	biological_process	pyridoxine biosynthetic process
C	0016740	molecular_function	transferase activity
C	0016769	molecular_function	transferase activity, transferring nitrogenous groups
C	0033856	molecular_function	pyridoxine 5'-phosphate synthase activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0008615	biological_process	pyridoxine biosynthetic process
D	0016740	molecular_function	transferase activity
D	0016769	molecular_function	transferase activity, transferring nitrogenous groups
D	0033856	molecular_function	pyridoxine 5'-phosphate synthase activity
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0008615	biological_process	pyridoxine biosynthetic process
E	0016740	molecular_function	transferase activity
E	0016769	molecular_function	transferase activity, transferring nitrogenous groups
E	0033856	molecular_function	pyridoxine 5'-phosphate synthase activity
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0008615	biological_process	pyridoxine biosynthetic process
F	0016740	molecular_function	transferase activity
F	0016769	molecular_function	transferase activity, transferring nitrogenous groups
F	0033856	molecular_function	pyridoxine 5'-phosphate synthase activity
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0008615	biological_process	pyridoxine biosynthetic process
G	0016740	molecular_function	transferase activity
G	0016769	molecular_function	transferase activity, transferring nitrogenous groups
G	0033856	molecular_function	pyridoxine 5'-phosphate synthase activity
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0008615	biological_process	pyridoxine biosynthetic process
H	0016740	molecular_function	transferase activity
H	0016769	molecular_function	transferase activity, transferring nitrogenous groups
H	0033856	molecular_function	pyridoxine 5'-phosphate synthase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	16
Details	BINDING SITE FOR RESIDUE PXP A 501

Chain	Residue
A	ASN9
A	GLY215
A	HIS216
A	HOH1046
A	HOH1177
A	HOH1353
A	HOH1439
B	ARG20
A	GLU72
A	VAL94
A	PHE133
A	GLU153
A	HIS193
A	GLY194
A	ASN213
A	ILE214

site_id	AC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PXP B 502

Chain	Residue
A	ARG20
B	ASN9
B	GLU72
B	VAL94
B	PHE133
B	GLU153
B	HIS193
B	GLY194
B	ASN213
B	ILE214
B	GLY215
B	HIS216
B	HOH1048
B	HOH1091
B	HOH1312

site_id	AC3
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PXP C 503

Chain	Residue
C	ASN9
C	GLU72
C	PHE133
C	GLU153
C	HIS193
C	GLY194
C	ASN213
C	ILE214
C	GLY215
C	HIS216
C	HOH1191
C	HOH1306
C	HOH1595
C	HOH1623
D	ARG20

site_id	AC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PXP D 504

Chain	Residue
C	ARG20
D	GLU72
D	VAL94
D	PHE133
D	GLU153
D	HIS193
D	GLY194
D	ASN213
D	ILE214
D	GLY215
D	HIS216
D	HOH1001
D	HOH1184
D	HOH1214
D	HOH1581

site_id	AC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE PXP E 505

Chain	Residue
E	ASN9
E	GLU72
E	PHE133
E	GLU153
E	HIS193
E	GLY194
E	ASN213
E	ILE214
E	GLY215
E	HIS216
E	HOH1083
E	HOH1567
E	HOH1626
F	ARG20

site_id	AC6
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PXP F 506

Chain	Residue
E	ARG20
E	SO4602
F	GLU72
F	PHE133
F	GLU153
F	HIS193
F	GLY194
F	ASN213
F	ILE214
F	GLY215
F	HIS216
F	HOH1188
F	HOH1235
F	HOH1244
F	HOH1538

site_id	AC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PXP G 507

Chain	Residue
G	HOH1352
G	HOH1518
G	HOH1519
G	HOH1617
G	HOH1627
H	ARG20
G	GLU72
G	PHE133
G	GLU153
G	HIS193
G	GLY194
G	ASN213
G	ILE214
G	GLY215
G	HIS216

site_id	AC8
Number of Residues	14
Details	BINDING SITE FOR RESIDUE PXP H 508

Chain	Residue
G	ARG20
H	GLU72
H	VAL94
H	PHE133
H	GLU153
H	HIS193
H	GLY194
H	ASN213
H	ILE214
H	GLY215
H	HIS216
H	HOH1115
H	HOH1245
H	HOH1493

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 C 601

Chain	Residue
C	HIS12
C	ARG47
C	ARG51
C	HIS52
C	HOH1191
C	HOH1624
D	ARG20

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 602

Chain	Residue
E	ARG20
E	HOH1539
F	HIS12
F	HIS52
F	PXP506
F	HOH1389
F	HOH1556

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 603

Chain	Residue
E	HIS12
E	ARG47
E	ARG51
E	HIS52
F	ARG20

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	16
Details	ACT_SITE: Proton acceptor => ECO:0000255\|HAMAP-Rule:MF_00279

Chain	Residue	Details
A	HIS45
A	GLU72
B	HIS45
B	GLU72
C	HIS45
C	GLU72
D	HIS45
D	GLU72
E	HIS45
E	GLU72
F	HIS45
F	GLU72
G	HIS45
G	GLU72
H	HIS45
H	GLU72

site_id	SWS_FT_FI2
Number of Residues	8
Details	ACT_SITE: Proton donor => ECO:0000255\|HAMAP-Rule:MF_00279

Chain	Residue	Details
A	HIS193
B	HIS193
C	HIS193
D	HIS193
E	HIS193
F	HIS193
G	HIS193
H	HIS193

site_id	SWS_FT_FI3
Number of Residues	64
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00279

Chain	Residue	Details
A	ASN9
C	ASN9
C	ASP11
C	ARG20
C	ARG47
C	HIS52
C	THR102
C	GLY194
C	GLY215
D	ASN9
D	ASP11
D	ARG20
D	ARG47
D	HIS52
D	THR102
D	GLY194
D	GLY215
E	ASN9
E	ASP11
E	ARG20
E	ARG47
E	HIS52
E	THR102
E	GLY194
E	GLY215
F	ASN9
F	ASP11
F	ARG20
F	ARG47
F	HIS52
F	THR102
F	GLY194
F	GLY215
G	ASN9
G	ASP11
G	ARG20
G	ARG47
G	HIS52
G	THR102
G	GLY194
G	GLY215
H	ASN9
H	ASP11
H	ARG20
H	ARG47
H	HIS52
H	THR102
H	GLY194
H	GLY215
A	ASP11
A	ARG20
A	ARG47
A	HIS52
A	THR102
A	GLY194
A	GLY215
B	ASN9
B	ASP11
B	ARG20
B	ARG47
B	HIS52
B	THR102
B	GLY194
B	GLY215

site_id	SWS_FT_FI4
Number of Residues	8
Details	SITE: Transition state stabilizer => ECO:0000255\|HAMAP-Rule:MF_00279

Chain	Residue	Details
A	GLU153
B	GLU153
C	GLU153
D	GLU153
E	GLU153
F	GLU153
G	GLU153
H	GLU153

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