Research workbench
Palmitoylated oprm outer membrane factor
Analyse Palmitoylated oprm outer membrane factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y1K
- Type
- protein
- Length
- 2,741 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Pseudomonas aeruginosa
- Molecule
- Outer membrane protein OprM
- UniProt
- Q51487
- Ligands
- PLM
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · resolution 3.8 · 2 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Outer membrane protein OprM | protein | 457 | 58% helix, 10% strand | Q51487 |
| E | Outer membrane protein OprM | protein | 456 | 53% helix, 10% strand | Q51487 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 3 copies · chains A, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.78 | 0.80 | 87 | empty |
| 2 | 1046 | 0.74 | 0.77 | 77 | empty |
| 3 | 53 | 0.65 | 0.94 | 16 | empty |
| 4 | 355 | 0.60 | 0.77 | 48 | empty |
| 5 | 346 | 0.59 | 0.77 | 65 | empty |
Interfaces
8 interfaces between chains.
- D–E · 2877 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2853 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2839 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2838 Ų buried · 42 hydrogen bonds · protein-protein
- D–F · 2791 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 lipid (palmitoylation).
Compared structures
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 4Y1K · PDBe 4Y1K · UniProt Q51487
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