5DB5 | pdb_00005db5

Crystal structure of PLP-bound E. coli SufS (cysteine persulfide intermediate) in space group P21

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d5db5b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	NifS-like protein/selenocysteine lyase	(Escherichia coli DH5[alpha] ) [TaxId: 668369 ],	SCOPe (2.08)
A	d5db5a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	NifS-like protein/selenocysteine lyase	(Escherichia coli DH5[alpha] ) [TaxId: 668369 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PLP-dependent transferases	8034378	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8034378	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)
B		e5db5B1	A: cradle loop barrel	X: RIFT-related	H: Alanine racemase-C	T: Lipocalin_7	F:	ECOD (20:10:01)
A		e5db5A1	A: cradle loop barrel	X: RIFT-related	H: Alanine racemase-C	T: Lipocalin_7	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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
A, B	Cysteine desulfurase	cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity carbon-sulfur lyase activity lyase activity cysteine sulfinate desulfinase activity vitamin binding cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity carbon-sulfur lyase activity lyase activity cysteine sulfinate desulfinase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding hydrolase activity selenocysteine lyase activity	cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular process cellular component organization or biogenesis oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular process cellular component organization or biogenesis oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process cysteine metabolic process metabolic process small molecule metabolic process sulfur compound metabolic process selenium compound metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site	Binding Site
A, B	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B	IPR010970	Cysteine desulfurase, SufS	Family
A, B	IPR000192	Aminotransferase class V domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.