Research workbench
Structural basis for maintenance of bacterial outer membrane lipid asymmetry
Analyse Structural basis for maintenance of bacterial outer membrane lipid asymmetry in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NUO
- Type
- protein
- Length
- 1,616 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein F; ABC transporter permease
- UniProt
- P02931, A0A0W8AQT6
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, E | Outer membrane protein F | protein | 340 | 4% helix, 60% strand | P02931 |
| D | ABC transporter permease | protein | 200 | 67% helix, 3% strand | A0A0W8AQT6 |
| B | ABC transporter permease | protein | 197 | 64% helix, 3% strand | A0A0W8AQT6 |
| F | ABC transporter permease | protein | 199 | 64% helix, 3% strand | A0A0W8AQT6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains C, E, A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 20 copies · chains C, D, F, A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.77 | 0.79 | 74 | empty |
| 2 | 1079 | 0.76 | 0.78 | 65 | C8E |
| 3 | 1121 | 0.76 | 0.78 | 65 | empty |
| 4 | 1056 | 0.71 | 0.75 | 68 | SO4 |
| 5 | 987 | 0.70 | 0.74 | 67 | SO4 |
Interfaces
9 interfaces between chains.
- C–E · 1531 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1527 Ų buried · 18 hydrogen bonds · protein-protein
- C–A · 1494 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 585 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 581 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5NUO · Structural basis for maintenance of bacterial outer membrane lipid asymmetry · the same entry in another collection · chain A against A, TM-score 1.00
- P02931 · AlphaFold monomer V2.0 prediction for outer membrane porin F (P02931) · a predicted model of the same protein · chain C 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 P02931
- Every structure of UniProt A0A0W8AQT6
- Elsewhere: RCSB PDB 5NUO · PDBe 5NUO · UniProt P02931 · UniProt A0A0W8AQT6
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