5FT8 | pdb_00005ft8

Crystal structure of the complex between the cysteine desulfurase CsdA and the sulfur-acceptor CsdE in the persulfurated state at 2.50 Angstroem resolution

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)
O	d5ft8o_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
M	d5ft8m_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
K	d5ft8k_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
I	d5ft8i_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G	d5ft8g_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d5ft8e_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d5ft8c_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d5ft8a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
O	SCOP2B Superfamily	PLP-dependent transferases	8083204	3000954	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	PLP-dependent transferases	8083204	3000954	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	PLP-dependent transferases	8083204	3000954	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	PLP-dependent transferases	8083204	3000954	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PLP-dependent transferases	8083204	3000954	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLP-dependent transferases	8083204	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8083204	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8083204	3000954	SCOP2B (2022-06-29)
N [auth c]	SCOP2B Superfamily	SufE/NifU	8033337	3000436	SCOP2B (2022-06-29)
L [auth a]	SCOP2B Superfamily	SufE/NifU	8033337	3000436	SCOP2B (2022-06-29)
J [auth Y]	SCOP2B Superfamily	SufE/NifU	8033337	3000436	SCOP2B (2022-06-29)
H [auth W]	SCOP2B Superfamily	SufE/NifU	8033337	3000436	SCOP2B (2022-06-29)
F [auth U]	SCOP2B Superfamily	SufE/NifU	8033337	3000436	SCOP2B (2022-06-29)
D [auth S]	SCOP2B Superfamily	SufE/NifU	8033337	3000436	SCOP2B (2022-06-29)
B [auth Q]	SCOP2B Superfamily	SufE/NifU	8033337	3000436	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)
O	Aminotran_5_C	e5ft8O1	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)
O	Aminotran_5_N	e5ft8O2	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)
M	Aminotran_5_C	e5ft8M2	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)
M	Aminotran_5_N	e5ft8M1	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)
K	Aminotran_5_C	e5ft8K2	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)
K	Aminotran_5_N	e5ft8K1	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)
I	Aminotran_5_C	e5ft8I1	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)
I	Aminotran_5_N	e5ft8I2	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)
G	Aminotran_5_C	e5ft8G2	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)
G	Aminotran_5_N	e5ft8G1	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)
E	Aminotran_5_C	e5ft8E1	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)
E	Aminotran_5_N	e5ft8E2	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	e5ft8C2	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	e5ft8C1	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	e5ft8A1	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	e5ft8A2	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)
O	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
O	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
M	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
M	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
K	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
K	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
I	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
I	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
G	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
G	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
E	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
E	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)
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, C, E, G, I A, C, E, G, I, K, M, O	PF02657	Fe-S metabolism associated domain (SufE)	Fe-S metabolism associated domain	-	Family
A, C, E, G, I A, C, E, G, I, K, M, O	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
B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], L [auth a], N [auth c], P [auth e]	PF02657	Fe-S metabolism associated domain (SufE)	Fe-S metabolism associated domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K, M, O	Cysteine desulfurase CsdA	cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity carbon-sulfur lyase activity lyase activity cysteine sulfinate desulfinase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity carbon-sulfur lyase activity lyase activity cysteine sulfinate desulfinase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding hydrolase activity selenocysteine lyase activity	oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular component organization or biogenesis oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular component organization or biogenesis catabolic process L-cysteine catabolic process L-cysteine metabolic process amino acid metabolic process organic acid catabolic process alpha-amino acid metabolic process carboxylic acid catabolic process amino acid catabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process cysteine metabolic process proteinogenic amino acid metabolic process sulfur compound catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process sulfur amino acid catabolic process cysteine catabolic process small molecule catabolic process selenocysteine catabolic process selenocysteine metabolic process localization transport sulfur compound transport establishment of localization	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex sulfurtransferase complex L-cysteine desulfurase complex transferase complex cytoplasm cytosol
B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], L [auth a], N [auth c], P [auth e]	Sulfur acceptor protein CsdE	sulfur carrier activity molecular carrier activity	tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification cyclic threonylcarbamoyladenosine biosynthetic process metabolic process cellular process macromolecule metabolic process RNA processing	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site	Binding Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR022471	Cysteine desulphurase, catalytic subunit, CsdA	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR010970	Cysteine desulfurase, SufS	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR000192	Aminotransferase class V domain	Domain
B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], L [auth a], N [auth c], P [auth e]	IPR017763	Cysteine desulfurase, sulphur acceptor subunit CsdE	Family
B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], L [auth a], N [auth c], P [auth e]	IPR003808	Fe-S metabolism associated domain, SufE-like	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C, E, G, I A, C, E, G, I, K, M, O	CSS	Parent Component: CYS RESID: AA0269 PSI-MOD : L-cysteine persulfide MOD:00274
B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], L [auth a], N [auth c], P [auth e]	CSS	Parent Component: CYS RESID: AA0269 , AA0269 PSI-MOD : L-cysteine persulfide MOD:00274 , 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.