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Crystal structure of the hydrophilic domain of respiratory complex I from thermus thermophilus, oxidized, 4 MOL/ASU, re-refined to 3.15 ångström resolution
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
- 3IAS
- Type
- protein
- Length
- 9,472 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
- 1.6.99.5
- UniProt
- Q56222, Q56221, Q56223, Q56220, Q56219, Q56218, Q56224, Q5SKZ7
- Ligands
- SF4, FES, FMN, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, A, J, S | NADH-quinone oxidoreductase subunit 1 (EC 1.6.99.5) | protein | 437 | 44% helix, 14% strand | Q56222 |
| 2, B, K, T | NADH-quinone oxidoreductase subunit 2 (EC 1.6.99.5) | protein | 178 | 44% helix, 10% strand | Q56221 |
| 3, C, L, U | NADH-quinone oxidoreductase subunit 3 (EC 1.6.99.5) | protein | 754 | 25% helix, 20% strand | Q56223 |
| 4, D, M, V | NADH-quinone oxidoreductase subunit 4 (EC 1.6.99.5) | protein | 377 | 47% helix, 11% strand | Q56220 |
| 5, E, N, W | NADH-quinone oxidoreductase subunit 5 (EC 1.6.99.5) | protein | 196 | 19% helix, 17% strand | Q56219 |
| 6, F, O, X | NADH-quinone oxidoreductase subunit 6 (EC 1.6.99.5) | protein | 145 | 35% helix, 13% strand | Q56218 |
| 9, G, P, Y | NADH-quinone oxidoreductase subunit 9 (EC 1.6.99.5) | protein | 154 | 17% helix, 23% strand | Q56224 |
| 7, H, Q, Z | 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 · 28 copies · chains 4, 6, 9, 3, 1, D, F, G, C, A, M, O, P, L, J, V, X, Y, U, S
- FES · Fe2/s2 (inorganic) cluster · ligand · 8 copies · chains 3, 1, 2, C, A, B, L, J, K, U, S, T
- FMN · Flavin mononucleotide · ligand · 4 copies · chains 1, A, J, S
- CA · Calcium ion · metal · 16 copies · chains 3, 5, 9, 2, 7, C, E, G, B, H, L, N, P, K, Q, U, W, Y, T, Z
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 | 1108 | 0.83 | 0.84 | 94 | empty |
| 2 | 1126 | 0.83 | 0.84 | 91 | empty |
| 3 | 1144 | 0.82 | 0.84 | 94 | empty |
| 4 | 1157 | 0.82 | 0.83 | 100 | empty |
| 5 | 671 | 0.78 | 0.83 | 63 | empty |
Interfaces
80 interfaces between chains.
- 4–5 · 2838 Ų buried · 55 hydrogen bonds · protein-protein
- V–W · 2834 Ų buried · 54 hydrogen bonds · protein-protein
- M–N · 2826 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 2826 Ų buried · 53 hydrogen bonds · protein-protein
- S–T · 2686 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3IAS · Crystal structure of the hydrophilic domain of respiratory complex I from Thermus… · 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 3IAS · PDBe 3IAS · UniProt Q56222 · UniProt Q56221 · UniProt Q56223 · UniProt Q56220 · UniProt Q56219 · UniProt Q56218 · UniProt Q56224 · UniProt Q5SKZ7
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