6WDU | pdb_00006wdu

The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	d6wdub_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase, beta-subunit	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d6wdua_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Tryptophan biosynthesis enzymes	Trp synthase alpha-subunit	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8032976	3001427	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8032560	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)
B	Ras	e6wduB1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Ras	ECOD (develop294)
A	Raptor_N	e6wduA1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Raptor_N	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00291	Pyridoxal-phosphate dependent enzyme (PALP)	Pyridoxal-phosphate dependent enzyme	-	Family
A	PF00290	Tryptophan synthase alpha chain (Trp_syntA)	Tryptophan synthase alpha chain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Tryptophan synthase beta chain	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity tryptophan synthase activity identical protein binding protein binding binding	oxoacid metabolic process indole-containing compound metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process biogenic amine biosynthetic process indole-containing compound biosynthetic process L-tryptophan metabolic process small molecule metabolic process indolalkylamine biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process oxoacid metabolic process indole-containing compound metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process biogenic amine biosynthetic process indole-containing compound biosynthetic process L-tryptophan metabolic process small molecule metabolic process indolalkylamine biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process L-tryptophan biosynthetic process proteinogenic amino acid metabolic process amine metabolic process amino acid biosynthetic process biosynthetic process amine biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process erythrose 4-phosphate/phosphoenolpyruvate family amino acid biosynthetic process biogenic amine metabolic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm
A	Tryptophan synthase alpha chain	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity tryptophan synthase activity	oxoacid metabolic process indole-containing compound metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process biogenic amine biosynthetic process indole-containing compound biosynthetic process L-tryptophan metabolic process small molecule metabolic process indolalkylamine biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process oxoacid metabolic process indole-containing compound metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process biogenic amine biosynthetic process indole-containing compound biosynthetic process L-tryptophan metabolic process small molecule metabolic process indolalkylamine biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process L-tryptophan biosynthetic process proteinogenic amino acid metabolic process amine metabolic process amino acid biosynthetic process biosynthetic process amine biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process erythrose 4-phosphate/phosphoenolpyruvate family amino acid biosynthetic process biogenic amine metabolic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR023026	Tryptophan synthase beta chain/beta chain-like	Family
B	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily	Homologous Superfamily
B	IPR006653	Tryptophan synthase, beta chain, conserved site	Conserved Site
B	IPR001926	Tryptophan synthase beta chain-like, PALP domain	Domain
B	IPR006654	Tryptophan synthase, beta chain	Family
A	IPR002028	Tryptophan synthase, alpha chain	Family
A	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A	IPR018204	Tryptophan synthase, alpha chain, active site	Active Site
A	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily

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.