5WT5 | pdb_00005wt5

L-homocysteine-bound NifS from Helicobacter pylori

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)
D	d5wt5d_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
C	d5wt5c_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
B	d5wt5b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
A	d5wt5a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Helicobacter pylori 26695 ) [TaxId: 85962 ],	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	8074680	3000954	SCOP2B (2022-06-29)
C	SCOP2 Family	Cystathionine synthase-like	8074679	4000672	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	PLP-dependent transferases	8074680	3000954	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8074680	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8074680	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)
D	Aminotran_5_C	e5wt5D2	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	e5wt5D1	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	Aminotran_5_C	e5wt5C1	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	e5wt5C2	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	e5wt5B2	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	e5wt5B1	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	e5wt5A2	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	e5wt5A1	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)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, 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
A, B, C, D	Cysteine desulfurase IscS	cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding cation binding metal ion binding	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 cellular process small molecule metabolic process sulfur compound metabolic process cellular component biogenesis cellular component organization 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 cellular process small molecule metabolic process sulfur compound metabolic process cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular component organization or biogenesis [2Fe-2S] cluster assembly	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR016454	Cysteine desulfurase	Family
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	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR000192	Aminotransferase class V domain	Domain
A, B, C, D	IPR010240	Cysteine desulfurase IscS	Family
A, B, C, D	IPR017773	Cysteine desulfurase NifS, proteobacteria	Family

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.