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Crystal structure of the hydrophilic domain of respiratory complex I from thermus thermophilus, reduced, 2 MOL/ASU, with bound NADH
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
- 3IAM
- Type
- protein
- Length
- 4,738 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, NAI, MG, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 34% 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 | 44% helix, 14% strand | Q56222 |
| 2, B | NADH-quinone oxidoreductase subunit 2 (EC 1.6.99.5) | protein | 179 | 45% helix, 11% strand | Q56221 |
| 3, C | NADH-quinone oxidoreductase subunit 3 (EC 1.6.99.5) | protein | 754 | 27% helix, 19% strand | Q56223 |
| 4, D | NADH-quinone oxidoreductase subunit 4 (EC 1.6.99.5) | protein | 378 | 47% helix, 10% strand | Q56220 |
| 5, E | NADH-quinone oxidoreductase subunit 5 (EC 1.6.99.5) | protein | 196 | 21% helix, 19% strand | Q56219 |
| 6, F | NADH-quinone oxidoreductase subunit 6 (EC 1.6.99.5) | protein | 144 | 37% helix, 12% strand | Q56218 |
| 9, G | NADH-quinone oxidoreductase subunit 9 (EC 1.6.99.5) | protein | 154 | 15% helix, 21% 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
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains 1, A
- MG · Magnesium ion · metal · 10 copies · chains 3, 7, 5, 1, 4, 2, C, H, E, A
- 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 | 1005 | 0.84 | 0.85 | 99 | MG |
| 2 | 1019 | 0.83 | 0.84 | 105 | empty |
| 3 | 749 | 0.78 | 0.82 | 65 | empty |
| 4 | 852 | 0.78 | 0.81 | 76 | FMN, NAI |
| 5 | 92 | 0.78 | 0.99 | 23 | empty |
Interfaces
35 interfaces between chains.
- D–E · 2865 Ų buried · 51 hydrogen bonds · protein-protein
- 4–5 · 2858 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2638 Ų buried · 48 hydrogen bonds · protein-protein
- 1–2 · 2634 Ų buried · 48 hydrogen bonds · protein-protein
- 1–3 · 1473 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3IAM · 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 3IAM · PDBe 3IAM · UniProt Q56222 · UniProt Q56221 · UniProt Q56223 · UniProt Q56220 · UniProt Q56219 · UniProt Q56218 · UniProt Q56224 · UniProt Q5SKZ7
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