Research workbench
Multidrug efflux pump adej with tp-6076 bound
Analyse Multidrug efflux pump adej with tp-6076 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RY3
- Type
- protein
- Length
- 3,140 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Efflux pump membrane transporter
- UniProt
- Q2FD94
- Ligands
- 80P
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 55% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Efflux pump membrane transporter | protein | 1047 | 55% helix, 18% strand | Q2FD94 |
| B | Efflux pump membrane transporter | protein | 1045 | 55% helix, 18% strand | Q2FD94 |
| C | Efflux pump membrane transporter | protein | 1048 | 54% helix, 19% strand | Q2FD94 |
Ligands and binding sites
- 80P · (4S,4aS,5aR,12aS)-4-(diethylamino)-3,10,12,12a-tetrahydroxy-1,11-dioxo-8-[(2S)-pyrrolidin-2-yl]-7-(trifluoromethyl)-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide · ligand · chains C
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 | 870 | 0.87 | 0.89 | 121 | empty |
| 2 | 854 | 0.85 | 0.87 | 91 | empty |
| 3 | 993 | 0.84 | 0.84 | 101 | 80P |
| 4 | 340 | 0.81 | 0.91 | 56 | empty |
| 5 | 432 | 0.81 | 0.89 | 63 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3092 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 3092 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2851 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7RY3 · Multidrug Efflux pump AdeJ with TP-6076 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 7RY3 · PDBe 7RY3 · UniProt Q2FD94
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