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	FSCD C-terminal domain-like	8093407	3002534	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Thioredoxin reductase-like	8084465	3000050	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	F_UNCLASSIFIED	e3vrdA2	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00034	e3vrdA1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: PF00034	ECOD (1.6)
B	PF09242	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: PF09242	ECOD (1.6)
B	PF07992	e3vrdB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF07992	ECOD (1.6)
B	PF21706	e3vrdB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF21706	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	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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Flavocytochrome c heme subunit	binding organic cyclic compound 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	-	periplasmic space cellular anatomical entity
B	Flavocytochrome c flavin subunit	oxidoreductase activity catalytic activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound 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	IPR009056	Cytochrome c-like domain	Domain
A	IPR024167	Cytochrome c4-like	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 R01GM133198.