MolNFT v1 · #172992 · protein
Deciphering the role of the channel constrictions in the opening mechanism of mexab-oprm efflux pump from pseudomonas aeruginosa
7AKZ · Outer membrane protein oprm: “Deciphering the role of the channel constrictions in the opening mechanism of mexab-oprm efflux pump from…”. X-ray diffraction, 1 ligand (PLM), 5 pockets (best druggability 0.72). MolNFT v1 #172992 on…
- PDB
- 7AKZ
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein oprm
- UniProt
- Q51487
- Ligands
- PLM
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer membrane protein oprm | protein | 455 | 60% helix, 12% strand | Q51487 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.72 | 0.76 | 67 | empty |
| 2 | 373 | 0.55 | 0.74 | 49 | empty |
| 3 | 53 | 0.31 | 0.76 | 10 | empty |
| 4 | 51 | 0.28 | 0.75 | 22 | empty |
| 5 | 51 | 0.27 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 360 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (palmitoylation).
Compared structures
- 7AKZ · Deciphering the role of the channel constrictions in the opening mechanism of MexAB-OprM… · the same entry in another collection · chain A against A, TM-score 1.00
- Q51487 · AlphaFold monomer V2.0 prediction for outer membrane protein oprm (Q51487) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q51487
- Elsewhere: RCSB PDB 7AKZ · PDBe 7AKZ · UniProt Q51487
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