MolNFT v1 · #67078 · protein
Crystal structure of the hydrophilic domain of respiratory complex I from thermus thermophilus, oxidized, 2 MOL/ASU
3I9V · NADH-quinone oxidoreductase subunit 1: “Crystal structure of the hydrophilic domain of respiratory complex I from thermus thermophilus, oxidized, 2…”. X-ray diffraction, 5 ligands (SF4, FES, FMN), 20 pockets (best druggability…
- PDB
- 3I9V
- Type
- protein
- Length
- 4,736 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase subunit 1; NADH-quinone oxidoreductase subunit 2…
- EC
- 1.6.99.5
- UniProt
- Q56222, Q56221, Q56223, Q56220, Q56219, Q56218, Q56224, Q5SKZ7
- Ligands
- SF4, FES, FMN, MN, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 33% helix, 16% 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 5 (EC 1.6.99.5) | protein | 196 | 19% helix, 17% strand | Q56219 |
| 6, F | NADH-quinone oxidoreductase subunit 6 (EC 1.6.99.5) | protein | 145 | 35% helix, 13% strand | Q56218 |
| 9, G | NADH-quinone oxidoreductase subunit 9 (EC 1.6.99.5) | protein | 154 | 18% helix, 19% strand | Q56224 |
| 7, H | NADH-quinone oxidoreductase subunit 15 (EC 1.6.99.5) | protein | 127 | 32% helix, 31% strand | Q5SKZ7 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 14 copies · chains 4, 6, 9, 3, 1, D, F, G, C, A
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains 3, 1, 2, C, A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains 1, A
- MN · Manganese (II) ion · metal · 12 copies · chains 3, 4, 7, 1, 2, 5, C, D, H, E
- CA · Calcium ion · metal · 2 copies · chains 3, 7, C, H
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 | 965 | 0.83 | 0.84 | 77 | empty |
| 2 | 1120 | 0.82 | 0.83 | 81 | MN |
| 3 | 794 | 0.80 | 0.83 | 77 | empty |
| 4 | 680 | 0.78 | 0.83 | 62 | empty |
| 5 | 861 | 0.77 | 0.80 | 79 | FMN |
Interfaces
35 interfaces between chains.
- D–E · 2849 Ų buried · 54 hydrogen bonds · protein-protein
- 4–5 · 2826 Ų buried · 53 hydrogen bonds · protein-protein
- 1–2 · 2667 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2663 Ų buried · 48 hydrogen bonds · protein-protein
- 1–3 · 1524 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3I9V · Crystal structure of the hydrophilic domain of respiratory complex I from Thermus… · the same entry in another collection · chain H against H, 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 3I9V · PDBe 3I9V · UniProt Q56222 · UniProt Q56221 · UniProt Q56223 · UniProt Q56220 · UniProt Q56219 · UniProt Q56218 · UniProt Q56224 · UniProt Q5SKZ7
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