MolNFT v1 · #93824 · protein
Crystal structure of the membrane domain of respiratory complex I from thermus thermophilus
4HE8 · NADH-quinone oxidoreductase subunit 7: “Crystal structure of the membrane domain of respiratory complex I from thermus thermophilus”. X-ray diffraction, 1 ligand (UMQ), 20 pockets (best druggability 0.77). MolNFT v1 #93824 on…
- PDB
- 4HE8
- Type
- protein
- Length
- 4,286 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase subunit 7; NADH-quinone oxidoreductase subunit 10…
- EC
- 1.6.5.3
- UniProt
- Q56217, Q56225, Q56226, Q56227, Q56228, Q56229, Q60019
- Ligands
- UMQ
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADH-quinone oxidoreductase subunit 7 (EC 1.6.5.3) | protein | 92 | 83% helix, 0% strand | Q56217 |
| J, D | NADH-quinone oxidoreductase subunit 10 (EC 1.6.5.3) | protein | 160 | 71% helix, 0% strand | Q56225 |
| K, E | NADH-quinone oxidoreductase subunit 11 (EC 1.6.5.3) | protein | 95 | 79% helix, 2% strand | Q56226 |
| L, F | NADH-quinone oxidoreductase subunit 12 (EC 1.6.5.3) | protein | 605 | 71% helix, 2% strand | Q56227 |
| M, G | NADH-quinone oxidoreductase subunit 13 (EC 1.6.5.3) | protein | 467 | 71% helix, 4% strand | Q56228 |
| N, I | NADH-quinone oxidoreductase subunit 14 (EC 1.6.5.3) | protein | 427 | 75% helix, 2% strand | Q56229 |
| H, C | NADH-quinone oxidoreductase subunit 8 (EC 1.6.5.3) | protein | 297 | 72% helix, 0% strand | Q60019 |
Ligands and binding sites
- UMQ · Undecyl-maltoside · ligand · 4 copies · chains A, J, N, L, M, B, D, I, F, 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 | 457 | 0.77 | 0.85 | 61 | empty |
| 2 | 891 | 0.77 | 0.79 | 70 | UMQ |
| 3 | 443 | 0.77 | 0.85 | 61 | empty |
| 4 | 880 | 0.76 | 0.79 | 66 | UMQ |
| 5 | 426 | 0.76 | 0.85 | 52 | empty |
Interfaces
32 interfaces between chains.
- J–K · 3420 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 3418 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 2515 Ų buried · 16 hydrogen bonds · protein-protein
- L–M · 2508 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 2478 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4HE8 · Crystal structure of the membrane domain of respiratory complex I from Thermus… · the same entry in another collection · chain D against D, 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 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 4HE8 · PDBe 4HE8 · UniProt Q56217 · UniProt Q56225 · UniProt Q56226 · UniProt Q56227 · UniProt Q56228 · UniProt Q56229 · UniProt Q60019
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