MolNFT v1 · #128521 · protein
Xenon for tunnelling analysis of the efflux pump component oprn.
5NSW · Multidrug efflux outer membrane protein oprn: “Xenon for tunnelling analysis of the efflux pump component oprn.”. X-ray diffraction, 4 ligands (PLM, NA, NI), 20 pockets (best druggability 0.65). MolNFT v1 #128521 on GenesisL1: 3D…
- PDB
- 5NSW
- Type
- protein
- Length
- 1,341 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux outer membrane protein oprn
- UniProt
- Q9I0Y7
- Ligands
- PLM, NA, NI, XE
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Multidrug efflux outer membrane protein oprn | protein | 445 | 66% helix, 14% strand | Q9I0Y7 |
| C | Multidrug efflux outer membrane protein oprn | protein | 451 | 66% helix, 14% strand | Q9I0Y7 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 6 copies · chains A, B, C
- NA · Sodium ion · metal · chains A, B
- NI · Nickel (II) ion · metal · chains C
- XE · Xenon · ion · 17 copies · chains A, B, C
- BOG · octyl beta-D-glucopyranoside · additive · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.65 | 0.74 | 61 | empty |
| 2 | 468 | 0.62 | 0.76 | 69 | empty |
| 3 | 83 | 0.49 | 0.83 | 21 | empty |
| 4 | 146 | 0.47 | 0.78 | 24 | empty |
| 5 | 84 | 0.42 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2875 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 2856 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2800 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 lipid (palmitoylation).
Compared structures
- 5NSW · Xenon for tunnelling analysis of the efflux pump component OprN. · 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 Q9I0Y7
- Elsewhere: RCSB PDB 5NSW · PDBe 5NSW · UniProt Q9I0Y7
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