Research workbench
Respiratory complex I from thermus thermophilus with bound decyl- ubiquinone
Analyse Respiratory complex I from thermus thermophilus with bound decyl- ubiquinone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I0D
- Type
- protein
- Length
- 9,550 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase subunit 1; NADH-quinone oxidoreductase subunit 2…
- EC
- 1.6.5.11
- UniProt
- Q56222, Q56221, Q56223, Q56220, Q56219, Q56218, Q56224, Q5SKZ7, Q5SI52, Q56217, Q56225, Q56226, Q56227, Q56228, Q56229, Q60019
- Ligands
- SF4, FES, FMN, DCQ
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 16 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, B | NADH-quinone oxidoreductase subunit 1 (EC 1.6.5.11) | protein | 437 | 45% helix, 13% strand | Q56222 |
| 2, C | NADH-quinone oxidoreductase subunit 2 (EC 1.6.5.11) | protein | 178 | 40% helix, 10% strand | Q56221 |
| 3, D | NADH-quinone oxidoreductase subunit 3 (EC 1.6.5.11) | protein | 756 | 27% helix, 20% strand | Q56223 |
| 4, E | NADH-quinone oxidoreductase subunit 4 (EC 1.6.5.11) | protein | 384 | 49% helix, 9% strand | Q56220 |
| 5, F | NADH-quinone oxidoreductase subunit 5 (EC 1.6.5.11) | protein | 196 | 22% helix, 20% strand | Q56219 |
| 6, G | NADH-quinone oxidoreductase subunit 6 (EC 1.6.5.11) | protein | 166 | 34% helix, 16% strand | Q56218 |
| 9, O | NADH-quinone oxidoreductase subunit 9 (EC 1.6.5.11) | protein | 180 | 24% helix, 18% strand | Q56224 |
| 7, I | NADH-quinone oxidoreductase subunit 15 (EC 1.6.5.11) | protein | 127 | 33% helix, 31% strand | Q5SKZ7 |
| W, X | NADH-quinone oxidoreductase subunit 16 | protein | 127 | 38% helix, 23% strand | Q5SI52 |
| A, P | NADH-quinone oxidoreductase subunit 7 (EC 1.6.5.11) | protein | 117 | 68% helix, 0% strand | Q56217 |
| J, R | NADH-quinone oxidoreductase subunit 10 (EC 1.6.5.11) | protein | 160 | 74% helix, 1% strand | Q56225 |
| K, S | NADH-quinone oxidoreductase subunit 11 (EC 1.6.5.11) | protein | 95 | 80% helix, 0% strand | Q56226 |
| L, T | NADH-quinone oxidoreductase subunit 12 (EC 1.6.5.11) | protein | 605 | 73% helix, 2% strand | Q56227 |
| M, U | NADH-quinone oxidoreductase subunit 13 (EC 1.6.5.11) | protein | 467 | 71% helix, 3% strand | Q56228 |
| N, V | NADH-quinone oxidoreductase subunit 14 (EC 1.6.5.11) | protein | 427 | 74% helix, 2% strand | Q56229 |
| H, Q | NADH-quinone oxidoreductase subunit 8 (EC 1.6.5.11) | protein | 353 | 64% helix, 1% strand | Q60019 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 14 copies · chains 1, 3, 4, 6, 9, B, D, E, G, O
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains 1, 2, 3, B, C, D
- FMN · Flavin mononucleotide · ligand · 2 copies · chains 1, B
- DCQ · 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione · ligand · 2 copies · chains 4, 6, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.88 | 0.89 | 101 | DCQ |
| 2 | 928 | 0.86 | 0.88 | 92 | DCQ |
| 3 | 1112 | 0.83 | 0.83 | 88 | empty |
| 4 | 1067 | 0.82 | 0.83 | 78 | empty |
| 5 | 1022 | 0.82 | 0.83 | 73 | empty |
Interfaces
83 interfaces between chains.
- J–K · 3314 Ų buried · 18 hydrogen bonds · protein-protein
- R–S · 3212 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 3124 Ų buried · 18 hydrogen bonds · protein-protein
- P–Q · 3008 Ų buried · 13 hydrogen bonds · protein-protein
- 4–5 · 2845 Ų buried · 59 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6I0D · Respiratory complex I from Thermus thermophilus with bound Decyl-Ubiqui · the same entry in another collection · chain W against W, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q56222
- Every structure of UniProt Q56221
- Every structure of UniProt Q56223
- Every structure of UniProt Q56220
- Every structure of UniProt Q56219
- Every structure of UniProt Q56218
- Every structure of UniProt Q56224
- Every structure of UniProt Q5SKZ7
- Every structure of UniProt Q5SI52
- Every structure of UniProt Q56217
- Every structure of UniProt Q56225
- Every structure of UniProt Q56226
- Every structure of UniProt Q56227
- Every structure of UniProt Q56228
- Every structure of UniProt Q56229
- Every structure of UniProt Q60019
- Elsewhere: RCSB PDB 6I0D · PDBe 6I0D · UniProt Q56222 · UniProt Q56221 · UniProt Q56223 · UniProt Q56220 · UniProt Q56219 · UniProt Q56218 · UniProt Q56224 · UniProt Q5SKZ7 · UniProt Q5SI52 · UniProt Q56217 · UniProt Q56225 · UniProt Q56226 · UniProt Q56227 · UniProt Q56228 · UniProt Q56229 · UniProt Q60019
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