Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4WY0

PdxS (G. stearothermophilus) co-crystallized with R5P in the presence of ammonia.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0006520	biological_process	amino acid metabolic process
A	0008615	biological_process	pyridoxine biosynthetic process
A	0016829	molecular_function	lyase activity
A	0016843	molecular_function	amine-lyase activity
A	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
A	0042819	biological_process	vitamin B6 biosynthetic process
A	0042823	biological_process	pyridoxal phosphate biosynthetic process
B	0006520	biological_process	amino acid metabolic process
B	0008615	biological_process	pyridoxine biosynthetic process
B	0016829	molecular_function	lyase activity
B	0016843	molecular_function	amine-lyase activity
B	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
B	0042819	biological_process	vitamin B6 biosynthetic process
B	0042823	biological_process	pyridoxal phosphate biosynthetic process
C	0006520	biological_process	amino acid metabolic process
C	0008615	biological_process	pyridoxine biosynthetic process
C	0016829	molecular_function	lyase activity
C	0016843	molecular_function	amine-lyase activity
C	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
C	0042819	biological_process	vitamin B6 biosynthetic process
C	0042823	biological_process	pyridoxal phosphate biosynthetic process
D	0006520	biological_process	amino acid metabolic process
D	0008615	biological_process	pyridoxine biosynthetic process
D	0016829	molecular_function	lyase activity
D	0016843	molecular_function	amine-lyase activity
D	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
D	0042819	biological_process	vitamin B6 biosynthetic process
D	0042823	biological_process	pyridoxal phosphate biosynthetic process
E	0006520	biological_process	amino acid metabolic process
E	0008615	biological_process	pyridoxine biosynthetic process
E	0016829	molecular_function	lyase activity
E	0016843	molecular_function	amine-lyase activity
E	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
E	0042819	biological_process	vitamin B6 biosynthetic process
E	0042823	biological_process	pyridoxal phosphate biosynthetic process
F	0006520	biological_process	amino acid metabolic process
F	0008615	biological_process	pyridoxine biosynthetic process
F	0016829	molecular_function	lyase activity
F	0016843	molecular_function	amine-lyase activity
F	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
F	0042819	biological_process	vitamin B6 biosynthetic process
F	0042823	biological_process	pyridoxal phosphate biosynthetic process
G	0006520	biological_process	amino acid metabolic process
G	0008615	biological_process	pyridoxine biosynthetic process
G	0016829	molecular_function	lyase activity
G	0016843	molecular_function	amine-lyase activity
G	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
G	0042819	biological_process	vitamin B6 biosynthetic process
G	0042823	biological_process	pyridoxal phosphate biosynthetic process
H	0006520	biological_process	amino acid metabolic process
H	0008615	biological_process	pyridoxine biosynthetic process
H	0016829	molecular_function	lyase activity
H	0016843	molecular_function	amine-lyase activity
H	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
H	0042819	biological_process	vitamin B6 biosynthetic process
H	0042823	biological_process	pyridoxal phosphate biosynthetic process
I	0006520	biological_process	amino acid metabolic process
I	0008615	biological_process	pyridoxine biosynthetic process
I	0016829	molecular_function	lyase activity
I	0016843	molecular_function	amine-lyase activity
I	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
I	0042819	biological_process	vitamin B6 biosynthetic process
I	0042823	biological_process	pyridoxal phosphate biosynthetic process
J	0006520	biological_process	amino acid metabolic process
J	0008615	biological_process	pyridoxine biosynthetic process
J	0016829	molecular_function	lyase activity
J	0016843	molecular_function	amine-lyase activity
J	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
J	0042819	biological_process	vitamin B6 biosynthetic process
J	0042823	biological_process	pyridoxal phosphate biosynthetic process
K	0006520	biological_process	amino acid metabolic process
K	0008615	biological_process	pyridoxine biosynthetic process
K	0016829	molecular_function	lyase activity
K	0016843	molecular_function	amine-lyase activity
K	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
K	0042819	biological_process	vitamin B6 biosynthetic process
K	0042823	biological_process	pyridoxal phosphate biosynthetic process
L	0006520	biological_process	amino acid metabolic process
L	0008615	biological_process	pyridoxine biosynthetic process
L	0016829	molecular_function	lyase activity
L	0016843	molecular_function	amine-lyase activity
L	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
L	0042819	biological_process	vitamin B6 biosynthetic process
L	0042823	biological_process	pyridoxal phosphate biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue CAC A 301

Chain	Residue
A	HIS115
A	ARG137
A	ARG138
A	HOH462
G	LYS187

site_id	AC2
Number of Residues	4
Details	binding site for residue PO4 B 301

Chain	Residue
B	GLY153
B	GLY214
B	GLY235
B	HOH426

site_id	AC3
Number of Residues	7
Details	binding site for residue R5P B 302

Chain	Residue
B	HIS115
B	ARG130
B	GLU134
B	ARG137
B	ARG138
B	HOH495
J	LYS187

site_id	AC4
Number of Residues	7
Details	binding site for residue CAC C 301

Chain	Residue
C	HIS115
C	GLU134
C	ARG137
C	ARG138
C	HOH476
C	HOH496
H	LYS187

site_id	AC5
Number of Residues	7
Details	binding site for residue EDO C 302

Chain	Residue
C	GLY85
C	ASP111
C	PHE114
C	HIS115
C	ILE116
C	HOH459
K	ARG165

site_id	AC6
Number of Residues	3
Details	binding site for residue PO4 D 301

Chain	Residue
D	GLY153
D	GLY214
D	HOH518

site_id	AC7
Number of Residues	6
Details	binding site for residue R5P D 302

Chain	Residue
D	HIS115
D	ARG130
D	GLU134
D	ARG137
D	ARG138
L	LYS187

site_id	AC8
Number of Residues	7
Details	binding site for residue R5P E 301

Chain	Residue
E	HIS115
E	ARG137
E	ARG138
E	HOH424
E	HOH450
E	HOH454
I	LYS187

site_id	AC9
Number of Residues	4
Details	binding site for residue PO4 F 301

Chain	Residue
F	3ZL81
F	GLY153
F	GLY214
F	HOH453

site_id	AD1
Number of Residues	3
Details	binding site for residue CAC F 302

Chain	Residue
F	ARG137
F	ARG138
K	LYS187

site_id	AD2
Number of Residues	8
Details	binding site for residue R5P G 301

Chain	Residue
A	LYS187
G	HIS115
G	ARG130
G	GLU134
G	ARG137
G	ARG138
G	EDO302
G	HOH442

site_id	AD3
Number of Residues	8
Details	binding site for residue EDO G 302

Chain	Residue
G	ILE84
G	GLU105
G	HIS115
G	GLY128
G	GLU134
G	ARG138
G	R5P301
G	HOH464

site_id	AD4
Number of Residues	7
Details	binding site for residue EDO G 303

Chain	Residue
A	ARG137
A	GLY190
G	VAL183
G	ALA186
G	LYS187
G	HOH460
G	HOH470

site_id	AD5
Number of Residues	4
Details	binding site for residue PO4 H 301

Chain	Residue
H	GLY153
H	GLY214
H	GLY235
H	HOH478

site_id	AD6
Number of Residues	4
Details	binding site for residue CAC H 302

Chain	Residue
C	LYS187
C	HOH465
H	ARG137
H	ARG138

site_id	AD7
Number of Residues	8
Details	binding site for residue R5P I 301

Chain	Residue
E	LYS187
I	GLU105
I	HIS115
I	ARG130
I	GLU134
I	ARG137
I	ARG138
I	HOH473

site_id	AD8
Number of Residues	7
Details	binding site for residue R5P J 301

Chain	Residue
B	LYS187
J	GLU105
J	HIS115
J	ARG130
J	GLU134
J	ARG137
J	ARG138

site_id	AD9
Number of Residues	8
Details	binding site for residue R5P K 301

Chain	Residue
F	LYS187
K	GLU105
K	HIS115
K	ARG130
K	GLU134
K	ARG137
K	ARG138
K	HOH453

site_id	AE1
Number of Residues	4
Details	binding site for residue CAC L 301

Chain	Residue
D	LYS187
L	ARG137
L	ARG138
L	HOH483

Functional Information from PROSITE/UniProt

site_id	PS01235
Number of Residues	19
Details	PDXS_SNZ_1 PdxS/SNZ family signature. LPVVNFAAGGVTTPADAAL

Chain	Residue	Details
B	LEU205-LEU223
A	LEU205-LEU223
F	LEU205-LEU223

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	ACT_SITE: Schiff-base intermediate with D-ribose 5-phosphate => ECO:0000255\|HAMAP-Rule:MF_01824, ECO:0000305\|PubMed:15911615

Chain	Residue	Details
F	3ZL81
D	LYS81
H	LYS81
G	L5P81
I	L5P81
J	L5P81
K	L5P81
L	L5P81

site_id	SWS_FT_FI2
Number of Residues	1
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_01824, ECO:0000305\|PubMed:15911615

Chain	Residue	Details
F	ASP24
D	ASP24
H	ASP24
G	ASP24
I	ASP24
J	ASP24
K	ASP24
L	ASP24

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_01824

Chain	Residue	Details
F	GLY153
H	ARG165
H	GLY214
H	GLY235
G	GLY153
G	ARG165
G	GLY214
G	GLY235
I	GLY153
I	ARG165
I	GLY214
F	ARG165
I	GLY235
J	GLY153
J	ARG165
J	GLY214
J	GLY235
K	GLY153
K	ARG165
K	GLY214
K	GLY235
L	GLY153
F	GLY214
L	ARG165
L	GLY214
L	GLY235
F	GLY235
D	GLY153
D	ARG165
D	GLY214
D	GLY235
H	GLY153

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