Research workbench
E. COLI NADH quinone oxidoreductase hydrophilic arm
Analyse E. COLI NADH quinone oxidoreductase hydrophilic arm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AWT
- Type
- protein
- Length
- 2,375 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase subunit B; NADH-quinone oxidoreductase subunit C/D…
- EC
- 7.1.1.-
- UniProt
- A0A4P6IQ32, A0A024L1E0, A0A5A4T568, A0A037YNA7, A0A037YPU0, A0A1X3LLK1
- Ligands
- SF4, FES, FMN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 33% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | NADH-quinone oxidoreductase subunit B (EC 7.1.1.-) | protein | 141 | 35% helix, 11% strand | A0A4P6IQ32 |
| D | NADH-quinone oxidoreductase subunit C/D (EC 7.1.1.-) | protein | 589 | 38% helix, 15% strand | A0A024L1E0 |
| E | NADH-quinone oxidoreductase subunit E | protein | 156 | 44% helix, 9% strand | A0A5A4T568 |
| F | NADH-quinone oxidoreductase subunit F (EC 7.1.1.-) | protein | 439 | 41% helix, 13% strand | A0A037YNA7 |
| G | NADH-quinone oxidoreductase (EC 7.1.1.-) | protein | 907 | 28% helix, 17% strand | A0A037YPU0 |
| I | NADH-quinone oxidoreductase subunit I | protein | 143 | 9% helix, 21% strand | A0A1X3LLK1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 7 copies · chains B, D, F, G, I
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, G
- FMN · Flavin mononucleotide · ligand · chains F
- MG · Magnesium ion · metal · 8 copies · chains E, G, I, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.82 | 0.83 | 96 | MG |
| 2 | 1048 | 0.81 | 0.82 | 106 | empty |
| 3 | 113 | 0.79 | 0.98 | 22 | empty |
| 4 | 960 | 0.78 | 0.80 | 84 | empty |
| 5 | 709 | 0.77 | 0.82 | 76 | FMN, MG |
Interfaces
13 interfaces between chains.
- E–F · 1964 Ų buried · 24 hydrogen bonds · protein-protein
- G–I · 1940 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1903 Ų buried · 11 hydrogen bonds · protein-protein
- B–I · 1869 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1842 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7AWT · E. coli NADH qui oxidoreductase hydrophilic arm · 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 A0A4P6IQ32
- Every structure of UniProt A0A024L1E0
- Every structure of UniProt A0A5A4T568
- Every structure of UniProt A0A037YNA7
- Every structure of UniProt A0A037YPU0
- Every structure of UniProt A0A1X3LLK1
- Elsewhere: RCSB PDB 7AWT · PDBe 7AWT · UniProt A0A4P6IQ32 · UniProt A0A024L1E0 · UniProt A0A5A4T568 · UniProt A0A037YNA7 · UniProt A0A037YPU0 · UniProt A0A1X3LLK1
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