Research workbench
The structure of ompf porin with a synthetic dibenzo-18-crown-6 as modulator
Analyse The structure of ompf porin with a synthetic dibenzo-18-crown-6 as modulator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FYX
- Type
- protein
- Length
- 340 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein F
- UniProt
- P02931
- Ligands
- 451
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein F | protein | 340 | 5% helix, 60% strand | P02931 |
Ligands and binding sites
- 451 · N-(6,7,9,10,17,18,20,21-octahydrodibenzo[b,k][1,4,7,10,13,16]hexaoxacyclooctadecin-2-yl)acetamide · ligand · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.69 | 0.75 | 68 | 451, EPE |
| 2 | 236 | 0.47 | 0.74 | 34 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3FYX · The Structure of OmpF porin with a synthetic dibenzo-18-crown-6 as modulator · 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 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 P02931
- Elsewhere: RCSB PDB 3FYX · PDBe 3FYX · UniProt P02931
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