4WY0 | pdb_00004wy0

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

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d4wy0f_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
H	d4wy0h_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
D	d4wy0d_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
B	d4wy0b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
L	d4wy0l_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
K	d4wy0k_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
J	d4wy0j_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
I	d4wy0i_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
G	d4wy0g_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
E	d4wy0e_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
C	d4wy0c_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
A	d4wy0a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8036029	3000216	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Ras	e4wy0F1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
H	Ras	e4wy0H1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
D	Ras	e4wy0D1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
B	Ras	e4wy0B1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
L	Ras	e4wy0L1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
K	Ras	e4wy0K1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
J	Ras	e4wy0J1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
I	Ras	e4wy0I1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
G	Ras	e4wy0G1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
E	Ras	e4wy0E1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
C	Ras	e4wy0C1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)
A	Ras	e4wy0A1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
H	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
L	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
K	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
J	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
I	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, H	PF01680	SOR/SNZ family (SOR_SNZ)	SOR/SNZ family	Members of this family are enzymes involved in a new pathway of pyridoxine/pyridoxal 5-phosphate biosynthesis [1]. This family was formerly known as UPF0019.	Domain
A, C, E, G, I A, C, E, G, I, J, K, L	PF01680	SOR/SNZ family (SOR_SNZ)	SOR/SNZ family	Members of this family are enzymes involved in a new pathway of pyridoxine/pyridoxal 5-phosphate biosynthesis [1]. This family was formerly known as UPF0019.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F	Pyridoxal biosynthesis lyase PdxS	amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity catalytic activity carbon-nitrogen lyase activity	pyridoxal 5'-phosphate biosynthetic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process pyridoxal 5'-phosphate biosynthetic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process pyridoxal 5'-phosphate metabolic process phosphorus metabolic process pyridoxine biosynthetic process pyridoxine metabolic process amino acid metabolic process primary metabolic process	-
B, D, H	Pyridoxal biosynthesis lyase PdxS	amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity catalytic activity carbon-nitrogen lyase activity	pyridoxal 5'-phosphate biosynthetic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process pyridoxal 5'-phosphate biosynthetic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process pyridoxal 5'-phosphate metabolic process phosphorus metabolic process pyridoxine biosynthetic process pyridoxine metabolic process amino acid metabolic process primary metabolic process	-
A, C, E, G, I A, C, E, G, I, J, K, L	Pyridoxal biosynthesis lyase PdxS	amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity catalytic activity carbon-nitrogen lyase activity	pyridoxal 5'-phosphate biosynthetic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process pyridoxal 5'-phosphate biosynthetic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process pyridoxal 5'-phosphate metabolic process phosphorus metabolic process pyridoxine biosynthetic process pyridoxine metabolic process amino acid metabolic process primary metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
F	IPR001852	Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ	Family
F	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
F	IPR033755	PdxS/SNZ N-terminal domain	Domain
B, D, H	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
B, D, H	IPR001852	Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ	Family
B, D, H	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
B, D, H	IPR033755	PdxS/SNZ N-terminal domain	Domain
A, C, E, G, I A, C, E, G, I, J, K, L	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, J, K, L	IPR001852	Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ	Family
A, C, E, G, I A, C, E, G, I, J, K, L	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, J, K, L	IPR033755	PdxS/SNZ N-terminal domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.