Research workbench
Deciphering the role of the channel constrictions in the opening mechanism of mexab-oprm efflux pump from pseudomonas aeruginosa
Analyse Deciphering the role of the channel constrictions in the opening mechanism of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZRE
- Type
- protein
- Length
- 912 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein oprm
- UniProt
- Q51487
- Ligands
- PLM, SO4
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein oprm | protein | 455 | 61% helix, 11% strand | Q51487 |
| B | Outer membrane protein oprm | protein | 457 | 59% helix, 12% strand | Q51487 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 11 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.58 | 0.75 | 29 | empty |
| 2 | 388 | 0.55 | 0.73 | 46 | empty |
| 3 | 308 | 0.54 | 0.75 | 28 | empty |
| 4 | 63 | 0.35 | 0.78 | 14 | empty |
| 5 | 61 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 261 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (palmitoylation).
Compared structures
- 6ZRE · 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 6ZRE · PDBe 6ZRE · UniProt Q51487
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