MolNFT v1 · #167438 · protein
Cryo-electron microscopy structures of a gonococcal multidrug efflux pump illuminate a mechanism of drug recognition with ampicillin
6VKS · Efflux pump membrane transporter: “Cryo-electron microscopy structures of a gonococcal multidrug efflux pump illuminate a mechanism of drug…”. Electron microscopy, 2 ligands (PTY, AIX), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 6VKS
- Type
- protein
- Length
- 3,131 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Efflux pump membrane transporter
- UniProt
- A0A4T9VBR9
- Ligands
- PTY, AIX
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Efflux pump membrane transporter | protein | 1049 | 48% helix, 16% strand | A0A4T9VBR9 |
| B | Efflux pump membrane transporter | protein | 1040 | 49% helix, 14% strand | A0A4T9VBR9 |
| C | Efflux pump membrane transporter | protein | 1042 | 49% helix, 16% strand | A0A4T9VBR9 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 17 copies · chains A, B, C
- AIX · (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · 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 | 1045 | 0.87 | 0.88 | 121 | empty |
| 2 | 1002 | 0.87 | 0.88 | 125 | empty |
| 3 | 1184 | 0.85 | 0.86 | 116 | empty |
| 4 | 490 | 0.79 | 0.87 | 57 | empty |
| 5 | 423 | 0.78 | 0.87 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3362 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 3281 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 2946 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6VKS · 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 6VKS · PDBe 6VKS · UniProt A0A4T9VBR9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.