2C1D | pdb_00002c1d

Crystal structure of SoxXA from P. pantotrophus

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)
A	d2c1da1	All alpha proteins	Cytochrome c	Cytochrome c	automated matches	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
C	d2c1dc1	All alpha proteins	Cytochrome c	Cytochrome c	automated matches	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
E	d2c1de1	All alpha proteins	Cytochrome c	Cytochrome c	automated matches	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
G	d2c1dg1	All alpha proteins	Cytochrome c	Cytochrome c	automated matches	automated matches	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d2c1db_	All alpha proteins	Cytochrome c	Cytochrome c	automated matches	automated matches	(Paracoccus pantotrophus ) [TaxId: 82367 ],	SCOPe (2.08)
D	d2c1dd_	All alpha proteins	Cytochrome c	Cytochrome c	automated matches	automated matches	(Paracoccus pantotrophus ) [TaxId: 82367 ],	SCOPe (2.08)
F	d2c1df_	All alpha proteins	Cytochrome c	Cytochrome c	automated matches	automated matches	(Paracoccus pantotrophus ) [TaxId: 82367 ],	SCOPe (2.08)
H	d2c1dh_	All alpha proteins	Cytochrome c	Cytochrome c	automated matches	automated matches	(Paracoccus pantotrophus ) [TaxId: 82367 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Monodomain cytochrome c	8088144	4000635	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cytochrome c	8088145	3000815	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Cytochrome c	8088145	3000815	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cytochrome c	8088145	3000815	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Cytochrome c	8088145	3000815	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)
A	thiosulf_SoxA	e2c1dA1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: thiosulf_SoxA	ECOD (1.6)
C	thiosulf_SoxA	e2c1dC1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: thiosulf_SoxA	ECOD (1.6)
E	thiosulf_SoxA	e2c1dE1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: thiosulf_SoxA	ECOD (1.6)
G	thiosulf_SoxA	e2c1dG1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: thiosulf_SoxA	ECOD (1.6)
B	Cytochrom_C	e2c1dB1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrom_C	ECOD (1.6)
D	Cytochrom_C	e2c1dD1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrom_C	ECOD (1.6)
F	Cytochrom_C	e2c1dF1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrom_C	ECOD (1.6)
H	Cytochrom_C	e2c1dH1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrom_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
C	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
E	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
G	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
B	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
D	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
F	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
H	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF21342	SoxA/TsdA, cytochrome c domain (SoxA-TsdA_cyt-c)	SoxA/TsdA, cytochrome c domain	This entry represents the first cytochrome c domain of SoxA and TsdA proteins, heme proteins involved in sulfur oxidation [1-5].	Domain
B, D, F, H	PF00034	Cytochrome c (Cytochrom_C)	Cytochrome c	The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	SOXA	oxidoreductase activity catalytic activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding oxidoreductase activity catalytic activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding thiosulfate-cyanide sulfurtransferase activity protein heterodimerization activity protein binding protein dimerization activity oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor zinc ion binding electron transfer activity	sulfur compound metabolic process metabolic process cellular process sulfur oxidation	cellular anatomical structure periplasmic space protein-containing complex cytochrome complex catalytic complex
B, D, F, H	SOXX	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR009056	Cytochrome c-like domain	Domain
A, C, E, G	IPR025710	L-cysteine S-thiosulfotransferase subunit SoxA	Family
B, D, F, H	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B, D, F, H	IPR009056	Cytochrome c-like domain	Domain
B, D, F, H	IPR030999	Sulfur oxidation c-type cytochrome SoxX	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C, E, G	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.