Research workbench
Crystal structure of ompf porin soaked in ciprofloxacin metaloantibiotic
Analyse Crystal structure of ompf porin soaked in ciprofloxacin metaloantibiotic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZHV
- Type
- protein
- Length
- 1,022 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane porin F
- UniProt
- P02931
- Ligands
- QLB, NA, MG
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Outer membrane porin F | protein | 341 | 2% helix, 62% strand | P02931 |
| C | Outer membrane porin F | protein | 340 | 2% helix, 62% strand | P02931 |
Ligands and binding sites
- QLB · 2-[2-(2-octoxyethoxy)ethoxy]ethanol · ligand · 7 copies · chains B, A, C
- NA · Sodium ion · metal · 12 copies · chains B, A, C
- MG · Magnesium ion · metal · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.71 | 0.75 | 85 | empty |
| 2 | 1104 | 0.71 | 0.75 | 68 | empty |
| 3 | 990 | 0.70 | 0.75 | 63 | NA |
| 4 | 298 | 0.52 | 0.74 | 41 | empty |
| 5 | 293 | 0.51 | 0.74 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1538 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1512 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1510 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6ZHV · Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic · the same entry in another collection · chain B against B, TM-score 1.00
- P02931 · AlphaFold monomer V2.0 prediction for outer membrane porin F (P02931) · a predicted model of the same protein · chain B 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 6ZHV · PDBe 6ZHV · UniProt P02931
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