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Crystal structure of anti-basigin Fab fragment
Analyse Crystal structure of anti-basigin Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D9Z
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of antibody Fab fragment; Heavy chain of antibody Fab fragment
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of antibody Fab fragment | protein | 217 | 7% helix, 50% strand | — |
| H | Heavy chain of antibody Fab fragment | protein | 208 | 6% helix, 52% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.62 | 0.75 | 62 | empty |
| 2 | 76 | 0.56 | 0.88 | 22 | empty |
| 3 | 149 | 0.44 | 0.75 | 31 | empty |
| 4 | 54 | 0.27 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 1747 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 7D9Z · Crystal structure of anti-basigin Fab fragment · the same entry in another collection · chain L against L, 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 7D9Z · PDBe 7D9Z
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