Research workbench
Respiratory complex I from escherichia COLI - focused refinement of membrane arm
Analyse Respiratory complex I from escherichia COLI - focused refinement of membrane arm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NYH
- Type
- protein
- Length
- 2,195 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase subunit a; NADH-quinone oxidoreductase subunit H…
- EC
- 7.1.1.-, 7.1.1.2, 1.6.5.11, 1.6.5.3, 1.6.99.5
- UniProt
- P0AFC3, P0AFD4, P0AFE0, F4VE45, A0A1V3W1N5, P0AFE8, P0AFF0
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH-quinone oxidoreductase subunit a (EC 7.1.1.-) | protein | 86 | 84% helix, 0% strand | P0AFC3 |
| H | NADH-quinone oxidoreductase subunit H (EC 7.1.1.-) | protein | 262 | 64% helix, 0% strand | P0AFD4 |
| J | NADH-quinone oxidoreductase subunit J (EC 7.1.1.-) | protein | 164 | 76% helix, 2% strand | P0AFE0 |
| K | NADH-quinone oxidoreductase subunit K (EC 7.1.1.2) | protein | 100 | 71% helix, 3% strand | F4VE45 |
| L | NADH-quinone oxidoreductase subunit L (EC 1.6.5.11, 1.6.5.3, 1.6.99.5) | protein | 612 | 71% helix, 4% strand | A0A1V3W1N5 |
| M | NADH-quinone oxidoreductase subunit M (EC 7.1.1.-) | protein | 504 | 70% helix, 2% strand | P0AFE8 |
| N | NADH-quinone oxidoreductase subunit N (EC 7.1.1.-) | protein | 467 | 73% helix, 1% strand | P0AFF0 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.83 | 0.84 | 145 | empty |
| 2 | 568 | 0.79 | 0.84 | 50 | empty |
| 3 | 711 | 0.77 | 0.81 | 51 | empty |
| 4 | 248 | 0.66 | 0.82 | 26 | empty |
| 5 | 542 | 0.66 | 0.76 | 46 | empty |
Interfaces
13 interfaces between chains.
- J–K · 3267 Ų buried · 18 hydrogen bonds · protein-protein
- L–M · 2574 Ų buried · 12 hydrogen bonds · protein-protein
- K–N · 1776 Ų buried · 10 hydrogen bonds · protein-protein
- M–N · 1709 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 1661 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7NYH · Respiratory complex I from Escherichia coli - focused refinement of membrane arm · the same entry in another collection · chain N against N, TM-score 1.00
- P0AFF0 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit N (P0AFF0) · a predicted model of the same protein · chain N against A, TM-score 0.98
- P0AFE8 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit M (P0AFE8) · a predicted model of the same protein · chain M against A, TM-score 0.97
- P0AFD4 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit H (P0AFD4) · a predicted model of the same protein · chain H against A, TM-score 0.95
- P0AFE0 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit J (P0AFE0) · a predicted model of the same protein · chain J against A, TM-score 0.90
- P0AFC3 · AlphaFold monomer V2.0 prediction for NADH-quinone oxidoreductase subunit a (P0AFC3) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 P0AFC3
- Every structure of UniProt P0AFD4
- Every structure of UniProt P0AFE0
- Every structure of UniProt F4VE45
- Every structure of UniProt A0A1V3W1N5
- Every structure of UniProt P0AFE8
- Every structure of UniProt P0AFF0
- Elsewhere: RCSB PDB 7NYH · PDBe 7NYH · UniProt P0AFC3 · UniProt P0AFD4 · UniProt P0AFE0 · UniProt F4VE45 · UniProt A0A1V3W1N5 · UniProt P0AFE8 · UniProt P0AFF0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.