Research workbench
Respiratory complex I from thermus thermophilus, NADH dataset, major state
Analyse Respiratory complex I from thermus thermophilus, NADH dataset, major state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZIY
- Type
- protein
- Length
- 4,646 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase subunit 1; NADH-quinone oxidoreductase subunit 2…
- EC
- 7.1.1.-
- UniProt
- Q56222, Q56221, Q56223, Q56220, Q56219, Q56218, Q56224, Q5SKZ7, Q56217, Q56225, Q56226, Q56227, Q56228, Q56229, Q60019
- Ligands
- SF4, FES, FMN, NAI
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 15 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | NADH-quinone oxidoreductase subunit 1 (EC 7.1.1.-) | protein | 437 | 41% helix, 13% strand | Q56222 |
| 2 | NADH-quinone oxidoreductase subunit 2 (EC 7.1.1.-) | protein | 178 | 43% helix, 11% strand | Q56221 |
| 3 | NADH-quinone oxidoreductase subunit 3 (EC 7.1.1.-) | protein | 754 | 27% helix, 19% strand | Q56223 |
| 4 | NADH-quinone oxidoreductase subunit 4 (EC 7.1.1.-) | protein | 384 | 49% helix, 11% strand | Q56220 |
| 5 | NADH-quinone oxidoreductase subunit 5 (EC 7.1.1.-) | protein | 196 | 20% helix, 17% strand | Q56219 |
| 6 | NADH-quinone oxidoreductase subunit 6 (EC 7.1.1.-) | protein | 166 | 34% helix, 13% strand | Q56218 |
| 9 | NADH-quinone oxidoreductase subunit 9 (EC 7.1.1.-) | protein | 180 | 23% helix, 22% strand | Q56224 |
| 7 | NADH-quinone oxidoreductase subunit 15 (EC 7.1.1.-) | protein | 127 | 33% helix, 29% strand | Q5SKZ7 |
| A | NADH-quinone oxidoreductase subunit 7 (EC 7.1.1.-) | protein | 117 | 64% helix, 0% strand | Q56217 |
| J | NADH-quinone oxidoreductase subunit 10 (EC 7.1.1.-) | protein | 160 | 73% helix, 0% strand | Q56225 |
| K | NADH-quinone oxidoreductase subunit 11 (EC 7.1.1.-) | protein | 95 | 76% helix, 2% strand | Q56226 |
| L | NADH-quinone oxidoreductase subunit 12 (EC 7.1.1.-) | protein | 605 | 71% helix, 2% strand | Q56227 |
| M | NADH-quinone oxidoreductase subunit 13 (EC 7.1.1.-) | protein | 467 | 73% helix, 3% strand | Q56228 |
| N | NADH-quinone oxidoreductase subunit 14 (EC 7.1.1.-) | protein | 427 | 74% helix, 1% strand | Q56229 |
| H | NADH-quinone oxidoreductase subunit 8 (EC 7.1.1.-) | protein | 353 | 65% helix, 0% strand | Q60019 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 7 copies · chains 1, 3, 4, 6, 9
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains 1, 2, 3
- FMN · Flavin mononucleotide · ligand · chains 1
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains 1
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 | 1166 | 0.88 | 0.89 | 106 | empty |
| 2 | 1125 | 0.82 | 0.83 | 85 | empty |
| 3 | 746 | 0.80 | 0.83 | 72 | empty |
| 4 | 945 | 0.77 | 0.80 | 82 | FMN, NAI |
| 5 | 954 | 0.76 | 0.78 | 67 | empty |
Interfaces
35 interfaces between chains.
- J–K · 3607 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 3372 Ų buried · 7 hydrogen bonds · protein-protein
- 4–5 · 2948 Ų buried · 38 hydrogen bonds · protein-protein
- 1–2 · 2814 Ų buried · 32 hydrogen bonds · protein-protein
- L–M · 2447 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ZIY · Respiratory complex I from Thermus thermophilus, NADH dataset, major state · the same entry in another collection · chain A against A, 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
- 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 6ZIY · PDBe 6ZIY · UniProt Q56222 · UniProt Q56221 · UniProt Q56223 · UniProt Q56220 · UniProt Q56219 · UniProt Q56218 · UniProt Q56224 · UniProt Q5SKZ7 · UniProt Q56217 · UniProt Q56225 · UniProt Q56226 · UniProt Q56227 · UniProt Q56228 · UniProt Q56229 · UniProt Q60019
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