5YU0 | pdb_00005yu0

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d5yu0d_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Streptomyces pristinaespiralis ) [TaxId: 38300 ],	SCOPe (2.08)
C	d5yu0c_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Streptomyces pristinaespiralis ) [TaxId: 38300 ],	SCOPe (2.08)
B	d5yu0b_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Streptomyces pristinaespiralis ) [TaxId: 38300 ],	SCOPe (2.08)
A	d5yu0a_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Streptomyces pristinaespiralis ) [TaxId: 38300 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ornithine cyclodeaminase-like	8063738	3000041	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ornithine cyclodeaminase-like	8063738	3000041	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ornithine cyclodeaminase-like	8063738	3000041	SCOP2B (2022-06-29)
A	SCOP2 Family	Ornithine cyclodeaminase-like	8063737	4000025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ornithine cyclodeaminase-like	8063738	3000041	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	OCD_Mu_crystall	e5yu0D1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: OCD_Mu_crystall	ECOD (v294.1)
C	OCD_Mu_crystall	e5yu0C1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: OCD_Mu_crystall	ECOD (v294.1)
B	OCD_Mu_crystall	e5yu0B1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: OCD_Mu_crystall	ECOD (v294.1)
A	TBP	e5yu0A1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: TBP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Lysine cyclodeaminase	ornithine cyclodeaminase activity lyase activity ammonia-lyase activity catalytic activity carbon-nitrogen lyase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR003462	Ornithine cyclodeaminase/mu-crystallin	Family
A, B, C, D	IPR023401	Ornithine cyclodeaminase, N-terminal	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.