3VRD

Crystal structure of flavocytochrome c from Thermochromatium tepidum

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	d3vrda1	All alpha proteins	Cytochrome c	Cytochrome c	Two-domain cytochrome c	automated matches	(Thermochromatium tepidum ) [TaxId: 1050 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Flavocytochrome c sulfide dehydrogenase	8084464	4000130	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Thioredoxin reductase-like	8084465	3000050	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	FSCD C-terminal domain-like	8093407	3002534	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)
A	Cytochrome_CBB3	e3vrdA1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
A	UNK_F_TYPE	e3vrdA2	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: UNK_F_TYPE	ECOD (1.6)
B	FCSD-flav_bind	e3vrdB2	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: FCSD-flav_bind	ECOD (1.6)
B	FCSD_central	e3vrdB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: FCSD_central	ECOD (1.6)
B	Pyr_redox_2	e3vrdB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	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)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	3.90.760.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C Sulfide Dehydrogenase	Chain A Domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
B	PF21706	Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain, central (FCSD_central)	Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain, central	This domain is located centrally in Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain from the proteobacteria Allochromatium vinosum, a component of the enzyme that catalyses the reversible conversion of sulphide to elemental sulfur in vit ...	This domain is located centrally in Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain from the proteobacteria Allochromatium vinosum, a component of the enzyme that catalyses the reversible conversion of sulphide to elemental sulfur in vitro. This domain is C-terminal to Pfam:PF07992 and N-terminal to Pfam:PF09242. This domain shows a five-stranded parallel beta-sheet flanked on one side by three alpha-helices and on the other side by a three-stranded anti parallel beta-sheet [1].	Domain
B	PF09242	Flavocytochrome c sulphide dehydrogenase, flavin-binding (FCSD-flav_bind)	Flavocytochrome c sulphide dehydrogenase, flavin-binding	Members of this family adopt a structure consisting of a beta(3,4)-alpha(3) core, and an alpha+beta sandwich. They are required for binding to flavin, and subsequent electron transfer [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Flavocytochrome c heme subunit	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	-	cellular anatomical structure periplasmic space
B	Flavocytochrome c flavin subunit	oxidoreductase activity catalytic activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
A	IPR050597	Cytochrome c Oxidase Subunit	Family
A	IPR009056	Cytochrome c-like domain	Domain
A	IPR024167	Cytochrome c4-like	Family
B	IPR052541	Sulfide-quinone oxidoreductase	Family
B	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
B	IPR015323	Flavocytochrome c sulphide dehydrogenase, flavin-binding	Domain
B	IPR023753	FAD/NAD(P)-binding domain	Domain
B	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily	Homologous Superfamily
B	IPR049386	Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain, central	Domain
B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
B	IPR037092	Flavocytochrome c sulphide dehydrogenase, flavin-binding domain superfamily	Homologous Superfamily
B	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
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.