3FKD | pdb_00003fkd

The crystal structure of L-threonine-O-3-phosphate decarboxylase from Porphyromonas gingivalis

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)
D	d3fkdd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Bacteroides gingivalis (Porphyromonas gingivalis ) [TaxId: 837 ],	SCOPe (2.08)
C	d3fkdc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Bacteroides gingivalis (Porphyromonas gingivalis ) [TaxId: 837 ],	SCOPe (2.08)
B	d3fkdb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Bacteroides gingivalis (Porphyromonas gingivalis ) [TaxId: 837 ],	SCOPe (2.08)
A	d3fkda_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	Bacteroides gingivalis (Porphyromonas gingivalis ) [TaxId: 837 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PLP-dependent transferases	8073126	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8073126	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8073126	3000954	SCOP2B (2022-06-29)
A	SCOP2 Family	AAT-like	8073125	4000670	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8073126	3000954	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Aminotran_3	e3fkdD1	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: Aminotran_3	ECOD (v294.1)
C	NusG	e3fkdC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
C	Ribosomal_L27	e3fkdC2	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Ribosomal_L27	ECOD (v294.1)
B	NusG	e3fkdB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: NusG	ECOD (v294.1)
B	Ribosomal_L27	e3fkdB2	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Ribosomal_L27	ECOD (v294.1)
A	zf-MYND	e3fkdA2	A: a/b three-layered sandwiches	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: zf-MYND	ECOD (v294.1)
A	Big_10	e3fkdA3	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Big_10	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00155	Aminotransferase class I and II (Aminotran_1_2)	Aminotransferase class I and II		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	L-threonine-O-3-phosphate decarboxylase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding	-	-

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	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D	IPR004839	Aminotransferase, class I/classII, large 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.