Research workbench
Multidrug efflux pump adej with eravacycline bound
Analyse Multidrug efflux pump adej with eravacycline bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M4P
- Type
- protein
- Length
- 3,142 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Efflux pump membrane transporter
- UniProt
- Q2FD94
- Ligands
- 3PE, YQM
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 54% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Efflux pump membrane transporter | protein | 1049 | 54% helix, 17% strand | Q2FD94 |
| B | Efflux pump membrane transporter | protein | 1047 | 54% helix, 19% strand | Q2FD94 |
| C | Efflux pump membrane transporter | protein | 1046 | 55% helix, 19% strand | Q2FD94 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains A, C, B
- YQM · Eravacycline · ligand · chains B
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 | 1160 | 0.86 | 0.87 | 132 | empty |
| 2 | 593 | 0.84 | 0.89 | 85 | empty |
| 3 | 424 | 0.83 | 0.91 | 62 | empty |
| 4 | 355 | 0.82 | 0.92 | 53 | empty |
| 5 | 456 | 0.82 | 0.89 | 50 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3069 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3061 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2894 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7M4P · Multidrug Efflux pump AdeJ with Eravacycline bound · 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 Q2FD94
- Elsewhere: RCSB PDB 7M4P · PDBe 7M4P · UniProt Q2FD94
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