Research workbench
Crystal structure of anti S-gatifloxacin antibody Fab fragment in complex with S-gatifloxacin
Analyse Crystal structure of anti S-gatifloxacin antibody Fab fragment in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F35
- Type
- protein
- Length
- 1,229 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment light chain; Antibody Fab fragment heavy chain
- Ligands
- GFN, NA, SO4, CL
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab fragment light chain | protein | 204 | 7% helix, 54% strand | — |
| B | Antibody Fab fragment heavy chain | protein | 212 | 6% helix, 53% strand | — |
| C | Antibody Fab fragment light chain | protein | 204 | 6% helix, 56% strand | — |
| D | Antibody Fab fragment heavy chain | protein | 209 | 6% helix, 53% strand | — |
| E | Antibody Fab fragment light chain | protein | 189 | 7% helix, 44% strand | — |
| F | Antibody Fab fragment heavy chain | protein | 211 | 6% helix, 53% strand | — |
Ligands and binding sites
- GFN · 1-cyclopropyl-6-fluoro-8-methoxy-7-[(3S)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid · ligand · 3 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains B, C, D, F
- CL · Chloride ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, B, F
- GOL · Glycerol · additive · 2 copies · chains C
- CIT · Citric acid · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.70 | 0.75 | 107 | NA |
| 2 | 602 | 0.62 | 0.74 | 52 | empty |
| 3 | 411 | 0.58 | 0.75 | 46 | empty |
| 4 | 295 | 0.54 | 0.75 | 27 | empty |
| 5 | 281 | 0.52 | 0.75 | 35 | EDO |
Interfaces
7 interfaces between chains.
- A–B · 1729 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1614 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1561 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 445 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 199 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7F35 · Crystal structure of anti S-gatifloxacin antibody Fab fragment in complex with… · 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 7F35 · PDBe 7F35
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