6EEW

Crystal structure of Catharanthus roseus tryptophan decarboxylase in complex with L-tryptophan

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6eewa_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Madagascar periwinkle (Catharanthus roseus ) [TaxId: 4058 ],	SCOPe (2.08)
B	d6eewb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Madagascar periwinkle (Catharanthus roseus ) [TaxId: 4058 ],	SCOPe (2.08)
C	d6eewc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Madagascar periwinkle (Catharanthus roseus ) [TaxId: 4058 ],	SCOPe (2.08)
D	d6eewd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Madagascar periwinkle (Catharanthus roseus ) [TaxId: 4058 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Pyridoxal-dependent decarboxylase	8083285	4003328	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8083286	3000954	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8083286	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8083286	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8083286	3000954	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)
A	Pyridoxal_deC	e6eewA2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Pyridoxal_deC	ECOD (1.6)
A	Aminotran_5_N	e6eewA1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
B	Pyridoxal_deC	e6eewB2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Pyridoxal_deC	ECOD (1.6)
B	Aminotran_5_N	e6eewB1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
C	Pyridoxal_deC	e6eewC2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Pyridoxal_deC	ECOD (1.6)
C	Aminotran_5_N	e6eewC1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
D	Pyridoxal_deC	e6eewD1	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Pyridoxal_deC	ECOD (1.6)
D	Aminotran_5_N	e6eewD2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00282	Pyridoxal-dependent decarboxylase conserved domain (Pyridoxal_deC)	Pyridoxal-dependent decarboxylase conserved domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Aromatic-L-amino-acid decarboxylase	aromatic-L-amino-acid decarboxylase activity 5-hydroxy-L-tryptophan decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding aromatic-L-amino-acid decarboxylase activity 5-hydroxy-L-tryptophan decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding L-tryptophan decarboxylase activity	oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process amino acid metabolic process primary metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D	IPR010977	Aromatic-L-amino-acid decarboxylase	Family
A, B, C, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D	IPR002129	Pyridoxal phosphate-dependent decarboxylase	Family
A, B, C, D	IPR021115	Pyridoxal-phosphate binding site	Binding Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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.