6H8K
Crystal structure of a variant (Q133C in PSST) of Yarrowia lipolytica complex I
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A [auth 1] | SCOP2 Family | NADH-quinone oxidoreductase subunit 8-like | 8067552 | 4005664 | SCOP2 (2022-06-29) |
A [auth 1] | SCOP2 Superfamily | Antiporter subunits half-channel-like | 8067553 | 3002280 | SCOP2 (2022-06-29) |
N [auth K] | SCOP2 Family | Nq06/HydA N-terminal domain-like | 8085724 | 4007641 | SCOP2 (2022-06-29) |
N [auth K] | SCOP2 Superfamily | Nqo6/HydA N-terminal domain-like | 8085725 | 3002291 | SCOP2 (2022-06-29) |
O [auth L] | SCOP2B Superfamily | NADH-quinone oxidoreductase, subunit 11-like | 8053510 | 3002200 | SCOP2B (2022-06-29) |
C [auth 3] | SCOP2 Family | NADH-ubiquinone oxidoreductase chain 3-like | 8085719 | 4005842 | SCOP2 (2022-06-29) |
C [auth 3] | SCOP2 Superfamily | NADH-quinone oxidoreductase, subunit 11-like | 8106708 | 3002200 | SCOP2 (2022-06-29) |
D [auth 4] | SCOP2B Superfamily | Antiporter subunits half-channel-like | 8071762 | 3002280 | SCOP2B (2022-06-29) |
D [auth 4] | SCOP2B Superfamily | Antiporter subunits half-channel-like | 8093347 | 3002280 | SCOP2B (2022-06-29) |
F [auth 6] | SCOP2B Superfamily | NADH-quinone oxidoreductase, subunit 11-like | 8053517 | 3002200 | SCOP2B (2022-06-29) |
I [auth C] | SCOP2 Family | Nqo4-like | 8085738 | 4000433 | SCOP2 (2022-06-29) |
I [auth C] | SCOP2 Superfamily | HydB/Nqo4-like | 8085739 | 3001849 | 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 [auth 1] | NADHdh | e6h8k11 | A: alpha complex topology | X: Sodium/proton antiporter subunits-like (From Homology) | H: Sodium/proton antiporter subunits-like | T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related | F: NADHdh | ECOD (1.6) |
K [auth G] | Complex1_30kDa | e6h8kG1 | A: a+b two layers | X: Nqo5-like | H: Nqo5-like (From Topology) | T: Nqo5-like | F: Complex1_30kDa | ECOD (1.6) |
M [auth I] | Fer4_21_1 | e6h8kI1 | A: a+b two layers | X: 4Fe-4S ferredoxin (From Topology) | H: 4Fe-4S ferredoxin (From Topology) | T: 4Fe-4S ferredoxin | F: Fer4_21_1 | ECOD (1.6) |
N [auth K] | Oxidored_q6 | e6h8kK1 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: CheY-like | F: Oxidored_q6 | ECOD (1.6) |
O [auth L] | Oxidored_q2 | e6h8kL1 | A: alpha complex topology | X: NADH-quinone oxidoreductase subunit K (From Topology) | H: NADH-quinone oxidoreductase subunit K (From Topology) | T: NADH-quinone oxidoreductase subunit K | F: Oxidored_q2 | ECOD (1.6) |
B [auth 2] | Proton_antipo_M | e6h8k21 | A: alpha complex topology | X: Sodium/proton antiporter subunits-like (From Homology) | H: Sodium/proton antiporter subunits-like | T: NADH-quinone oxidoreductase subunit L (NuoL)-related | F: Proton_antipo_M | ECOD (1.6) |
C [auth 3] | Oxidored_q4 | e6h8k31 | A: extended segments | X: NADH-quinone oxidoreductase subunit A (From Topology) | H: NADH-quinone oxidoreductase subunit A (From Topology) | T: NADH-quinone oxidoreductase subunit A | F: Oxidored_q4 | ECOD (1.6) |
D [auth 4] | Proton_antipo_M | e6h8k41 | A: alpha complex topology | X: Sodium/proton antiporter subunits-like (From Homology) | H: Sodium/proton antiporter subunits-like | T: NADH-quinone oxidoreductase subunit L (NuoL)-related | F: Proton_antipo_M | ECOD (1.6) |
E [auth 5] | Proton_antipo_M | e6h8k51 | A: alpha complex topology | X: Sodium/proton antiporter subunits-like (From Homology) | H: Sodium/proton antiporter subunits-like | T: NADH-quinone oxidoreductase subunit L (NuoL)-related | F: Proton_antipo_M | ECOD (1.6) |
F [auth 6] | Oxidored_q3 | e6h8k61 | A: extended segments | X: NADH-quinone oxidoreductase subunit J (From Topology) | H: NADH-quinone oxidoreductase subunit J (From Topology) | T: NADH-quinone oxidoreductase subunit J | F: Oxidored_q3 | ECOD (1.6) |
G [auth A] | F_UNCLASSIFIED | e6h8kA6 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: F_UNCLASSIFIED | ECOD (1.6) |
G [auth A] | PRK09129 | e6h8kA3 | A: a+b two layers | X: 4Fe-4S ferredoxin (From Topology) | H: 4Fe-4S ferredoxin (From Topology) | T: 4Fe-4S ferredoxin | F: PRK09129 | ECOD (1.6) |
G [auth A] | Fer2_4 | e6h8kA2 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Ubiquitin-like | F: Fer2_4 | ECOD (1.6) |
G [auth A] | F_UNCLASSIFIED | e6h8kA7 | A: a+b two layers | X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology) | H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domain 1 | F: F_UNCLASSIFIED | ECOD (1.6) |
G [auth A] | F_UNCLASSIFIED | e6h8kA4 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology) | T: Formate dehydrogenase/DMSO reductase, domains 2 and 3 | F: F_UNCLASSIFIED | ECOD (1.6) |
G [auth A] | NADH-G_4Fe-4S_3 | e6h8kA1 | A: extended segments | X: iron-sulfur center-binding helical hairpin (From Topology) | H: iron-sulfur center-binding helical hairpin (From Topology) | T: iron-sulfur center-binding helical hairpin | F: NADH-G_4Fe-4S_3 | ECOD (1.6) |
H [auth B] | NADH_4Fe-4S | e6h8kB1 | A: alpha bundles | X: Bromodomain-like | H: Nqo1C-terminal domain-like (From Topology) | T: Nqo1C-terminal domain-like | F: NADH_4Fe-4S | ECOD (1.6) |
H [auth B] | F_UNCLASSIFIED | e6h8kB3 | A: a+b two layers | X: beta-Grasp | H: Ubiquitin-related | T: Nqo1 middle domain-like | F: F_UNCLASSIFIED | ECOD (1.6) |
H [auth B] | Complex1_51K | e6h8kB2 | A: a/b three-layered sandwiches | X: Nqo1 FMN-binding domain-like (From Topology) | H: Nqo1 FMN-binding domain-like (From Topology) | T: Nqo1 FMN-binding domain-like | F: Complex1_51K | ECOD (1.6) |
I [auth C] | Complex1_49kDa_1st | e6h8kC2 | A: alpha complex topology | X: 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 subunit | F: Complex1_49kDa_1st | ECOD (1.6) |
I [auth C] | NuoD | e6h8kC3 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NuoD | ECOD (1.6) |
I [auth C] | Complex1_49kDa_2nd | e6h8kC1 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: Complex1_49kDa_2nd | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth 1] | PF00146 | NADH dehydrogenase (NADHdh) | NADH dehydrogenase | - | Family |
K [auth G] | PF00329 | Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa) | Respiratory-chain NADH dehydrogenase, 30 Kd subunit | - | Family |
M [auth I] | PF12838 | 4Fe-4S dicluster domain (Fer4_7) | 4Fe-4S dicluster domain | 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 contai ... | Domain |
N [auth K] | PF01058 | NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6) | NADH ubiquinone oxidoreductase, 20 Kd subunit | - | Family |
O [auth L] | PF00420 | NADH-ubiquinone/plastoquinone oxidoreductase chain 4L (Oxidored_q2) | NADH-ubiquinone/plastoquinone oxidoreductase chain 4L | - | Family |
B [auth 2] | PF00361 | Proton-conducting membrane transporter (Proton_antipo_M) | Proton-conducting membrane transporter | - | Family |
C [auth 3] | PF00507 | NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 (Oxidored_q4) | NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 | - | Family |
D [auth 4] | PF00361 | Proton-conducting membrane transporter (Proton_antipo_M) | Proton-conducting membrane transporter | - | Family |
E [auth 5] | PF00361 | Proton-conducting membrane transporter (Proton_antipo_M) | Proton-conducting membrane transporter | - | Family |
E [auth 5] | PF00662 | NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus (Proton_antipo_N) | NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus | - | Family |
F [auth 6] | PF00499 | NADH-ubiquinone/plastoquinone oxidoreductase chain 6 (Oxidored_q3) | NADH-ubiquinone/plastoquinone oxidoreductase chain 6 | - | Family |
G [auth A] | PF13510 | 2Fe-2S iron-sulfur cluster binding domain (Fer2_4) | 2Fe-2S iron-sulfur cluster binding domain | The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ... | Domain |
G [auth A] | PF22117 | NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain (Nqo3_Fer4) | NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain | NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contain ... | Domain |
G [auth A] | PF10588 | NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3) | NADH-ubiquinone oxidoreductase-G iron-sulfur binding region | - | Domain |
H [auth B] | PF22461 | SLBB domain (SLBB_2) | SLBB domain | This entry represents a set of SLBB domains [5]. | Domain |
H [auth B] | PF01512 | Respiratory-chain NADH dehydrogenase 51 Kd subunit (Complex1_51K) | Respiratory-chain NADH dehydrogenase 51 Kd subunit | - | Family |
H [auth B] | PF10589 | NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S) | NADH-ubiquinone oxidoreductase-F iron-sulfur binding region | - | Domain |
I [auth C] | PF00346 | Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa) | Respiratory-chain NADH dehydrogenase, 49 Kd subunit | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Membrane Protein Annotation: OPM OPM Database Homepage
Chains | External Link | Type | Class | Superfamily | Family |
---|---|---|---|---|---|
OPM | Transmembrane | Alpha-helical polytopic | Electron transport chain complex I (NADH dehydrogenase) and supercomplexes | H+ or Na+ translocating NADH dehydrogenase |