5ODR | pdb_00005odr

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 2 minutes.


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
FSCOP2B SuperfamilyHydB/Nqo4-like 8096642 3001849 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyHydB/Nqo4-like 8096642 3001849 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AFer4_21_1e5odrA3 A: a+b two layersX: 4Fe-4S ferredoxin (From Topology)H: 4Fe-4S ferredoxin (From Topology)T: 4Fe-4S ferredoxinF: Fer4_21_1ECOD (1.6)
AFAD_binding_3_1ste5odrA1 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: FAD_binding_3_1stECOD (1.6)
APyr_redox_2e5odrA2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: Pyr_redox_2ECOD (1.6)
GFer4_21_1e5odrG3 A: a+b two layersX: 4Fe-4S ferredoxin (From Topology)H: 4Fe-4S ferredoxin (From Topology)T: 4Fe-4S ferredoxinF: Fer4_21_1ECOD (1.6)
GFAD_binding_3_1ste5odrG1 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: FAD_binding_3_1stECOD (1.6)
GPyr_redox_2e5odrG2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: Pyr_redox_2ECOD (1.6)
HCoB_CoM_SS_B_likee5odrH2 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: ATC-likeF: CoB_CoM_SS_B_likeECOD (1.6)
HUNK_F_TYPEe5odrH1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: ATC-likeF: UNK_F_TYPEECOD (1.6)
BCoB_CoM_SS_B_likee5odrB1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: ATC-likeF: CoB_CoM_SS_B_likeECOD (1.6)
BUNK_F_TYPEe5odrB2 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: ATC-likeF: UNK_F_TYPEECOD (1.6)
FNiFeSe_Hases_1ste5odrF4 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: NiFeSe_Hases_1stECOD (1.6)
FNiFeSe_Hases_3rde5odrF3 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rdECOD (1.6)
FNiFeSe_Hases_3rd_1e5odrF2 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rd_1ECOD (1.6)
LNiFeSe_Hases_1ste5odrL4 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: NiFeSe_Hases_1stECOD (1.6)
LNiFeSe_Hases_3rde5odrL3 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rdECOD (1.6)
LNiFeSe_Hases_3rd_1e5odrL1 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rd_1ECOD (1.6)
EOxidored_q6e5odrE2 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: CheY-likeF: Oxidored_q6ECOD (1.6)
EUNK_F_TYPEe5odrE1 A: few secondary structure elementsX: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunitF: UNK_F_TYPEECOD (1.6)
KOxidored_q6e5odrK1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: CheY-likeF: Oxidored_q6ECOD (1.6)
KUNK_F_TYPEe5odrK2 A: few secondary structure elementsX: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunitF: UNK_F_TYPEECOD (1.6)
DUNK_F_TYPEe5odrD1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Methyl-viologen reducing hydrogenase subunit D (From Topology)T: Methyl-viologen reducing hydrogenase subunit DF: UNK_F_TYPEECOD (1.6)
JUNK_F_TYPEe5odrJ1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Methyl-viologen reducing hydrogenase subunit D (From Topology)T: Methyl-viologen reducing hydrogenase subunit DF: UNK_F_TYPEECOD (1.6)
CFer4_8e5odrC1 A: alpha arraysX: alpha-helical ferredoxin-likeH: alpha-helical ferredoxin (From Topology)T: alpha-helical ferredoxinF: Fer4_8ECOD (1.6)
IFer4_8e5odrI1 A: alpha arraysX: alpha-helical ferredoxin-likeH: alpha-helical ferredoxin (From Topology)T: alpha-helical ferredoxinF: Fer4_8ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, G
PF131874Fe-4S dicluster domain (Fer4_9)4Fe-4S dicluster domain- Family
A, G
PF128384Fe-4S dicluster domain (Fer4_7)4Fe-4S dicluster domainSuperfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.
Domain
A, G
PF00890FAD binding domain (FAD_binding_2)FAD binding domainThis family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase. Domain
B, H
PF02754Cysteine-rich domain (CCG)Cysteine-rich domainThe key element of this domain is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins [2]. There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In so ...The key element of this domain is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins [2]. There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In some instances one of the cysteines is replaced by an aspartate, and aspartate can in principle also function as a ligand of an iron-sulfur cluster [2]. The entry includes a subunit from heterodisulphide reductase and a subunit from glycolate oxidase (Swiss:P52074) [1] and glycerol-3-phosphate dehydrogenase.
Domain
F, L
PF00374Nickel-dependent hydrogenase (NiFeSe_Hases)Nickel-dependent hydrogenase- Family
E, K
PF01058NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)NADH ubiquinone oxidoreductase, 20 Kd subunitDomain
D, J
PF02662Methyl-viologen-reducing hydrogenase, delta subunit (FlpD)Methyl-viologen-reducing hydrogenase, delta subunit- Family
C, I
PF131834Fe-4S dicluster domain (Fer4_8)4Fe-4S dicluster domainSuperfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, G
Heterodisulfide reductase, subunit A - -
B, H
Heterodisulfide reductase, subunit B -
F, L
Methyl-viologen reducing hydrogenase, subunit A - -
E, K
Methyl-viologen reducing hydrogenase, subunit G - -
D, J
Methyl-viologen reducing hydrogenase, subunit D - -
C, I
Heterodisulfide reductase, subunit C