Research workbench
Cation selective pathway of ompf porin revealed by anomalous X-ray diffraction
Analyse Cation selective pathway of ompf porin revealed by anomalous X-ray diffraction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HW9
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein F
- UniProt
- P02931
- Ligands
- K, CL
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer membrane protein F | protein | 339 | 4% helix, 59% strand | P02931 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains B
- CL · Chloride ion · ion · 2 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.70 | 0.74 | 64 | P6G, K, CL |
| 2 | 937 | 0.70 | 0.75 | 70 | P6G, K, CL |
| 3 | 210 | 0.46 | 0.74 | 33 | empty |
| 4 | 227 | 0.46 | 0.73 | 32 | empty |
| 5 | 68 | 0.42 | 0.80 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 613 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HW9 · Cation selective pathway of OmpF porin revealed by anomalous x-ray 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 3HW9 · PDBe 3HW9 · UniProt P02931
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