Research workbench
Salmonella typhi ompf complex with ciprofloxacin
Analyse Salmonella typhi ompf complex with ciprofloxacin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KRA
- Type
- protein
- Length
- 1,018 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein F
- Ligands
- CPF
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein F | protein | 341 | 3% helix, 50% strand | — |
| B | Outer membrane protein F | protein | 340 | 3% helix, 51% strand | — |
| C | Outer membrane protein F | protein | 337 | 3% helix, 53% strand | — |
Ligands and binding sites
- CPF · 1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydroquinoline-3-carboxylic acid · ligand · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.81 | 0.90 | 42 | empty |
| 2 | 1168 | 0.70 | 0.75 | 117 | empty |
| 3 | 1007 | 0.70 | 0.74 | 76 | empty |
| 4 | 766 | 0.68 | 0.75 | 56 | CPF |
| 5 | 101 | 0.60 | 0.87 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1521 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1487 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1435 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4KRA · Salmonella typhi OmpF complex with Ciprofloxacin · 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
- Elsewhere: RCSB PDB 4KRA · PDBe 4KRA
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