MolNFT v1 · #114021 · protein
Crystal structure of a membrane protein from pseudomonas aeruginosa
5AZP · Multidrug efflux outer membrane protein oprn: “Crystal structure of a membrane protein from pseudomonas aeruginosa”. X-ray diffraction, 3 ligands (3PK, OYA, NA), 20 pockets (best druggability 0.69). MolNFT v1 #114021 on GenesisL1…
- PDB
- 5AZP
- Type
- protein
- Length
- 1,340 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
- 3PK, OYA, NA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug efflux outer membrane protein oprn | protein | 446 | 66% helix, 14% strand | Q9I0Y7 |
| B | Multidrug efflux outer membrane protein oprn | protein | 450 | 66% helix, 14% strand | Q9I0Y7 |
| C | Multidrug efflux outer membrane protein oprn | protein | 444 | 66% helix, 14% strand | Q9I0Y7 |
Ligands and binding sites
- 3PK · (2S)-1-(pentanoyloxy)propan-2-yl hexanoate · ligand · 2 copies · chains A, C
- OYA · Octanal · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- FMT · Formic acid · additive · 18 copies · chains A, C, B
- GOL · Glycerol · additive · 12 copies · chains A, C, B
- ACT · Acetate ion · additive · 9 copies · chains A, B, C
- BOG · octyl beta-D-glucopyranoside · additive · 8 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.69 | 0.75 | 87 | FMT, GOL |
| 2 | 397 | 0.57 | 0.75 | 53 | empty |
| 3 | 189 | 0.52 | 0.78 | 35 | empty |
| 4 | 161 | 0.47 | 0.77 | 33 | empty |
| 5 | 181 | 0.46 | 0.75 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2859 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 2832 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 2806 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
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 5AZP · PDBe 5AZP · UniProt Q9I0Y7
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