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Crystal structure of the hydrophilic domain of respiratory complex I from thermus thermophilus
Analyse Crystal structure of the hydrophilic domain of respiratory complex I from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FUG
- Type
- protein
- Length
- 9,332 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase chain 1; NADH-quinone oxidoreductase chain 2; NADH-quinone…
- EC
- 1.6.99.5
- UniProt
- Q56222, Q56221, Q56223, Q56220, Q56219, Q56218, Q56224
- Ligands
- SF4, FES, FMN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 33% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, A, J, S | NADH-quinone oxidoreductase chain 1 (EC 1.6.99.5) | protein | 432 | 42% helix, 15% strand | Q56222 |
| 2, B, K, T | NADH-quinone oxidoreductase chain 2 (EC 1.6.99.5) | protein | 178 | 43% helix, 9% strand | Q56221 |
| 3, C, L, U | NADH-quinone oxidoreductase chain 3 (EC 1.6.99.5) | protein | 737 | 27% helix, 16% strand | Q56223 |
| 4, D, M, V | NADH-quinone oxidoreductase chain 4 (EC 1.6.99.5) | protein | 370 | 41% helix, 7% strand | Q56220 |
| 5, E, N, W | NADH-quinone oxidoreductase chain 5 (EC 1.6.99.5) | protein | 191 | 16% helix, 17% strand | Q56219 |
| 6, F, O, X | NADH-quinone oxidoreductase chain 6 (EC 1.6.99.5) | protein | 144 | 40% helix, 10% strand | Q56218 |
| 9, G, P, Y | NADH-quinone oxidoreductase chain 9 (EC 1.6.99.5) | protein | 154 | 15% helix, 21% strand | Q56224 |
| 7, H, Q, Z | Conserved hypothetical protein | protein | 127 | 34% helix, 31% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 28 copies · chains 1, 3, 4, 6, 9, A, C, D, F, G, J, L, M, O, P, S, U, V, X, Y
- FES · Fe2/s2 (inorganic) cluster · ligand · 8 copies · chains 1, 2, 3, B, C, K, L, S, T, U
- FMN · Flavin mononucleotide · ligand · 4 copies · chains 1, A, J, S
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 | 1068 | 0.83 | 0.84 | 89 | empty |
| 2 | 1103 | 0.82 | 0.83 | 81 | empty |
| 3 | 1100 | 0.82 | 0.83 | 87 | empty |
| 4 | 1074 | 0.82 | 0.83 | 79 | empty |
| 5 | 746 | 0.77 | 0.82 | 75 | FMN |
Interfaces
81 interfaces between chains.
- 4–5 · 2824 Ų buried · 45 hydrogen bonds · protein-protein
- V–W · 2814 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 2813 Ų buried · 41 hydrogen bonds · protein-protein
- M–N · 2807 Ų buried · 44 hydrogen bonds · protein-protein
- 1–2 · 2666 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2FUG · Crystal structure of the hydrophilic domain of respiratory complex I from Thermus… · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 2FUG · PDBe 2FUG · UniProt Q56222 · UniProt Q56221 · UniProt Q56223 · UniProt Q56220 · UniProt Q56219 · UniProt Q56218 · UniProt Q56224
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