3GZD | pdb_00003gzd

Human selenocysteine lyase, P1 crystal form

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	PLP-dependent transferases	8074686	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8074686	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8074686	3000954	SCOP2B (2022-06-29)
A	SCOP2 Family	Cystathionine synthase-like	8074685	4000672	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8074686	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)
C	Aminotran_5_C	e3gzdC3	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: Aminotran_5_C	ECOD (1.6)
C	Aminotran_5_N	e3gzdC2	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	Aminotran_5_C	e3gzdD3	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: Aminotran_5_C	ECOD (1.6)
D	Aminotran_5_N	e3gzdD2	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	Aminotran_5_C	e3gzdB3	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: Aminotran_5_C	ECOD (1.6)
B	Aminotran_5_N	e3gzdB2	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)
A	Aminotran_5_C	e3gzdA3	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: Aminotran_5_C	ECOD (1.6)
A	Aminotran_5_N	e3gzdA2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	1.10.260.50	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)		CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	1.10.260.50	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)		CATH (4.3.0)
D	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	1.10.260.50	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)		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	1.10.260.50	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)		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
C	PF00266	Aminotransferase class-V (Aminotran_5)	Aminotransferase class-V	This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-.	Domain
A, B, D	PF00266	Aminotransferase class-V (Aminotran_5)	Aminotransferase class-V	This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Selenocysteine lyase	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity carbon-sulfur lyase activity lyase activity catalytic activity selenocysteine lyase activity vitamin binding vitamin B6 binding heterocyclic compound binding small molecule binding amino acid binding identical protein binding protein binding binding protein homodimerization activity protein dimerization activity carbon-sulfur lyase activity lyase activity catalytic activity selenocysteine lyase activity vitamin binding vitamin B6 binding heterocyclic compound binding small molecule binding amino acid binding transferase activity	catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process selenocysteine catabolic process alpha-amino acid metabolic process selenocysteine metabolic process alpha-amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process selenocysteine catabolic process alpha-amino acid metabolic process selenocysteine metabolic process alpha-amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cytosol protein-containing complex catalytic complex
A, B, D	Selenocysteine lyase	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity carbon-sulfur lyase activity lyase activity catalytic activity selenocysteine lyase activity vitamin binding vitamin B6 binding heterocyclic compound binding small molecule binding amino acid binding identical protein binding protein binding binding protein homodimerization activity protein dimerization activity carbon-sulfur lyase activity lyase activity catalytic activity selenocysteine lyase activity vitamin binding vitamin B6 binding heterocyclic compound binding small molecule binding amino acid binding transferase activity	catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process selenocysteine catabolic process alpha-amino acid metabolic process selenocysteine metabolic process alpha-amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process selenocysteine catabolic process alpha-amino acid metabolic process selenocysteine metabolic process alpha-amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cytosol protein-containing complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR016454	Cysteine desulfurase	Family
C	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
C	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
C	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
C	IPR000192	Aminotransferase class V domain	Domain
A, B, D	IPR016454	Cysteine desulfurase	Family
A, B, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, D	IPR000192	Aminotransferase class V domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q96I15	lung cancer malignant mesothelioma
A, B, D	Pharos: Q96I15	lung cancer malignant mesothelioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, D	CSS	Parent Component: CYS RESID: AA0269 PSI-MOD : L-cysteine persulfide MOD:00274

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.