Research workbench
Crystal structure of anti S-gatifloxacin antibody Fab fragment apo form
Analyse Crystal structure of anti S-gatifloxacin antibody Fab fragment apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F2S
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment heavy chain; Antibody Fab fragment light chain
- Ligands
- SO4, CL
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab fragment heavy chain | protein | 213 | 6% helix, 54% strand | — |
| B | Antibody Fab fragment light chain | protein | 202 | 8% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.66 | 0.75 | 61 | GOL |
| 2 | 214 | 0.58 | 0.80 | 34 | empty |
| 3 | 61 | 0.56 | 0.89 | 17 | GOL |
| 4 | 110 | 0.48 | 0.80 | 28 | empty |
| 5 | 100 | 0.39 | 0.76 | 15 | GOL, SO4 |
Interfaces
1 interface between chains.
- A–B · 1657 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7F2S · Crystal structure of anti S-gatifloxacin antibody Fab fragment apo form · 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 7F2S · PDBe 7F2S
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