MolNFT v1 · #129556 · protein
Trimeric ompu structure
5ONU · Outer membrane protein ompu: “Trimeric ompu structure”. X-ray diffraction, 12 pockets (best druggability 0.73). MolNFT v1 #129556 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ONU
- Type
- protein
- Length
- 960 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein ompu
- UniProt
- A0A1V9N7P1
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Outer membrane protein ompu | protein | 320 | 4% helix, 63% strand | A0A1V9N7P1 |
Ligands and binding sites
- LDA · Lauryl dimethylamine-N-oxide · additive · 10 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.73 | 0.96 | 16 | empty |
| 2 | 903 | 0.68 | 0.74 | 88 | GOL |
| 3 | 880 | 0.68 | 0.74 | 94 | GOL |
| 4 | 624 | 0.64 | 0.75 | 56 | GOL |
| 5 | 206 | 0.57 | 0.80 | 27 | C8E |
Interfaces
3 interfaces between chains.
- B–C · 2013 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2011 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2005 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5ONU · Trimeric OmpU structure · 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 A0A1V9N7P1
- Elsewhere: RCSB PDB 5ONU · PDBe 5ONU · UniProt A0A1V9N7P1
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