Respiratory complex I from Paracoccus denitrificans
Ivanov, B.S., Bridges, H.R., Hirst, J., Jarman, O.D.To be published.
Experimental Data Snapshot
Starting Model: in silico
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wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase subunit K | A [auth K] | 101 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B482 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B482  Go to UniProtKB:  A1B482 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B482 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase | B [auth G] | 674 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | |
UniProt | |||||
Find proteins for A1B489 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B489  Go to UniProtKB:  A1B489 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B489 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Protein-L-isoaspartate O-methyltransferase | C [auth t] | 217 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for A1B5L6 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B5L6  Go to UniProtKB:  A1B5L6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B5L6 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase subunit I | D [auth I] | 163 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B486 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B486  Go to UniProtKB:  A1B486 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B486 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH dehydrogenase subunit E | 239 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 1.6.5.3 | ||
UniProt | |||||
Find proteins for A1B494 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B494  Go to UniProtKB:  A1B494 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B494 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 6 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase subunit N | F [auth N] | 499 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B479 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B479  Go to UniProtKB:  A1B479 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B479 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 7 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase subunit H | G [auth H] | 345 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B487 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B487  Go to UniProtKB:  A1B487 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B487 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 8 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase subunit F | H [auth F] | 431 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 | |
UniProt | |||||
Find proteins for A1B491 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B491  Go to UniProtKB:  A1B491 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B491 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 9 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase subunit D | I [auth D] | 412 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B495 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B495  Go to UniProtKB:  A1B495 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B495 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 10 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH:ubiquinone oxidoreductase 17.2 kD subunit | J [auth q] | 124 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for A1B1H8 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B1H8  Go to UniProtKB:  A1B1H8 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B1H8 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 11 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase subunit A | K [auth A] | 121 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B498 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B498  Go to UniProtKB:  A1B498 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B498 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 12 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase chain 10 | L [auth J] | 200 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B483 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B483  Go to UniProtKB:  A1B483 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B483 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 13 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Zinc finger CHCC-type domain-containing protein | M [auth R] | 62 | Paracoccus denitrificans PD1222 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for A1B357 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B357  Go to UniProtKB:  A1B357 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B357 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 14 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
ETC complex I subunit conserved region | N [auth Q] | 103 | Paracoccus denitrificans PD1222 | Mutation(s): 0  Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B1M0 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B1M0  Go to UniProtKB:  A1B1M0 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B1M0 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 15 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase subunit C | O [auth C] | 208 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B496 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B496  Go to UniProtKB:  A1B496 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B496 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 16 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH-quinone oxidoreductase subunit B | P [auth B] | 175 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 7.1.1 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B497 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B497  Go to UniProtKB:  A1B497 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B497 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 17 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH dehydrogenase subunit L | Q [auth L] | 703 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 1.6.5.3 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B481 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B481  Go to UniProtKB:  A1B481 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B481 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 18 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NADH dehydrogenase subunit M | R [auth M] | 513 | Paracoccus denitrificans PD1222 | Mutation(s): 0  EC: 1.6.5.3 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for A1B480 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B480  Go to UniProtKB:  A1B480 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A1B480 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 12 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CDL Query on CDL | JA [auth H], LB [auth M] | CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L | |||
U10 Query on U10 | YA [auth B] | UBIQUINONE-10 C59 H90 O4 ACTIUHUUMQJHFO-UPTCCGCDSA-N | |||
P5S Query on P5S | CB [auth L], Z [auth I] | O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine C42 H82 N O10 P TZCPCKNHXULUIY-RGULYWFUSA-N | |||
PC1 Query on PC1 | QA [auth D], UA [auth J] | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N | |||
3PE Query on 3PE | CA [auth N] DB [auth L] EA [auth N] FA [auth N] HB [auth M] | 1,2-Distearoyl-sn-glycerophosphoethanolamine C41 H82 N O8 P LVNGJLRDBYCPGB-LDLOPFEMSA-N | |||
3PH Query on 3PH | AB [auth L] BB [auth L] DA [auth N] EB [auth L] FB [auth L] | 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C39 H77 O8 P YFWHNAWEOZTIPI-DIPNUNPCSA-N | |||
FMN Query on FMN | OA [auth F] | FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N | |||
SF4 Query on SF4 | PA [auth F] S [auth G] T [auth G] W [auth I] X [auth I] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N | |||
FES Query on FES | BA [auth E], U [auth G] | FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N | |||
ZN Query on ZN | XA [auth R] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | AA [auth I], HA [auth N], OB [auth M], RA [auth D] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
NA Query on NA | V [auth G] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Modified Residues 2 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
2MR Query on 2MR | I [auth D] | L-PEPTIDE LINKING | C8 H18 N4 O2 | ARG | |
FME Query on FME | K [auth A] | L-PEPTIDE LINKING | C6 H11 N O3 S | MET |
Task | Software Package | Version |
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RECONSTRUCTION | RELION | 3.1.0 |
MODEL REFINEMENT | PHENIX | 1.2 |
Funding Organization | Location | Grant Number |
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Medical Research Council (MRC, United Kingdom) | United Kingdom | MC_UU_00015/2 |
Medical Research Council (MRC, United Kingdom) | United Kingdom | MC_UU_00028/1 |