Research workbench
Crystal structure of respiratory complex I from Thermus thermophilus
Analyse Crystal structure of respiratory complex I from Thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M9S
- Type
- protein
- Length
- 8,122 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.5
- Source
- Thermus thermophilus
- Molecule
- NADH-quinone oxidoreductase subunit 1; NADH-quinone oxidoreductase subunit 2…
- EC
- 1.6.99.5, 1.6.5.3
- UniProt
- Q56222, Q56221, Q56223, Q56220, Q56219, Q56218, Q56224, Q5SKZ7
- Ligands
- SF4, FES, FMN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 4.5 · 13 distinct chains · 19% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, A | NADH-quinone oxidoreductase subunit 1 (EC 1.6.99.5) | protein | 437 | 43% helix, 14% strand | Q56222 |
| 2, B | NADH-quinone oxidoreductase subunit 2 (EC 1.6.99.5) | protein | 178 | 43% helix, 9% strand | Q56221 |
| 3, C | NADH-quinone oxidoreductase subunit 3 (EC 1.6.99.5) | protein | 754 | 25% helix, 20% strand | Q56223 |
| 4, D | NADH-quinone oxidoreductase subunit 4 (EC 1.6.99.5) | protein | 377 | 48% helix, 9% strand | Q56220 |
| 5, E | NADH-quinone oxidoreductase subunit C (EC 1.6.99.5) | protein | 196 | 19% helix, 17% strand | Q56219 |
| 6, F | NADH-quinone oxidoreductase subunit B (EC 1.6.99.5) | protein | 145 | 35% helix, 13% strand | Q56218 |
| 9, G | NADH-quinone oxidoreductase subunit I (EC 1.6.99.5) | protein | 154 | 18% helix, 19% strand | Q56224 |
| 7, J | NADH-quinone oxidoreductase subunit 15 (EC 1.6.99.5) | protein | 127 | 32% helix, 31% strand | Q5SKZ7 |
| L, O | NADH-quinone oxidoreductase subunit 12 (EC 1.6.99.5) | protein | 469 | 0% helix, 0% strand | — |
| M, P | NADH-quinone oxidoreductase subunit 13 (EC 1.6.5.3) | protein | 391 | 0% helix, 0% strand | — |
| N, Q | NADH-quinone oxidoreductase subunit 14 (EC 1.6.5.3) | protein | 378 | 0% helix, 0% strand | — |
| R, S | NADH-quinone oxidoreductase subunits 7, 10 and 11 (EC 1.6.5.3) | protein | 274 | 0% helix, 0% strand | — |
| H, T | NADH-quinone oxidoreductase subunit 8 (EC 1.6.5.3) | protein | 181 | 0% helix, 0% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 14 copies · chains 1, 3, 4, 6, 9, A, C, D, F, G
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains 1, 2, 3, A, B, C
- FMN · Flavin mononucleotide · ligand · 2 copies · chains 1, A
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 | 1141 | 0.82 | 0.83 | 77 | empty |
| 2 | 1169 | 0.81 | 0.83 | 80 | empty |
| 3 | 747 | 0.77 | 0.82 | 67 | empty |
| 4 | 87 | 0.77 | 0.98 | 23 | empty |
| 5 | 745 | 0.77 | 0.81 | 60 | empty |
Interfaces
53 interfaces between chains.
- 4–5 · 2834 Ų buried · 53 hydrogen bonds · protein-protein
- D–E · 2826 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 2668 Ų buried · 47 hydrogen bonds · protein-protein
- 1–2 · 2662 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 1527 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3M9S · Crystal structure of respiratory complex I from thermus thermophilus · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 3M9S · PDBe 3M9S · UniProt Q56222 · UniProt Q56221 · UniProt Q56223 · UniProt Q56220 · UniProt Q56219 · UniProt Q56218 · UniProt Q56224 · UniProt Q5SKZ7
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