Research workbench
Cryo-electron microscopy structures of a gonococcal multidrug efflux pump illuminate a mechanism of erythromycin drug recognition
Analyse Cryo-electron microscopy structures of a gonococcal multidrug efflux pump… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VKT
- Type
- protein
- Length
- 3,122 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Efflux pump membrane transporter
- UniProt
- A0A4T9VBR9
- Ligands
- PTY, ERY
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Efflux pump membrane transporter | protein | 1037 | 51% helix, 17% strand | A0A4T9VBR9 |
| B | Efflux pump membrane transporter | protein | 1043 | 51% helix, 17% strand | A0A4T9VBR9 |
| C | Efflux pump membrane transporter | protein | 1042 | 51% helix, 17% strand | A0A4T9VBR9 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 23 copies · chains A, C, B
- ERY · Erythromycin A · 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 | 1139 | 0.87 | 0.88 | 139 | empty |
| 2 | 751 | 0.85 | 0.88 | 96 | empty |
| 3 | 906 | 0.84 | 0.86 | 98 | empty |
| 4 | 393 | 0.77 | 0.87 | 40 | empty |
| 5 | 863 | 0.76 | 0.80 | 89 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3172 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 3149 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2873 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6VKT · Cryo-electron microscopy structures of a gonococcal multidrug efflux pump illuminate a… · 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 A0A4T9VBR9
- Elsewhere: RCSB PDB 6VKT · PDBe 6VKT · UniProt A0A4T9VBR9
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