Research workbench
Cation selective pathway of OmpF porin revealed by anomalous diffraction
Analyse Cation selective pathway of OmpF porin revealed by anomalous diffraction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HWB
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Escherichia coli
- Molecule
- Outer membrane protein F
- UniProt
- P02931
- Ligands
- RB
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · resolution 3 · 1 distinct chain · 4% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer membrane protein F | protein | 340 | 4% helix, 59% strand | P02931 |
Ligands and binding sites
- RB · Rubidium ion · metal · 19 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.71 | 0.75 | 71 | RB, P6G |
| 2 | 1002 | 0.71 | 0.75 | 65 | RB |
| 3 | 264 | 0.50 | 0.74 | 37 | RB, P6G |
| 4 | 261 | 0.49 | 0.74 | 36 | empty |
| 5 | 182 | 0.44 | 0.73 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 603 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HWB · Cation selective pathway of ompf porin revealed by anomalous diffraction · 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 3HWB · PDBe 3HWB · UniProt P02931
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