Research workbench
Crystal structure of the Fab fragment of B5209B, a murine monoclonal antibody specific for the fifth immunoglobulin domain (IG5) of human ROBO1
Analyse Crystal structure of the Fab fragment of B5209B, a murine monoclonal antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A76
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of the anti-human ROBO1 antibody B5209B Fab; Heavy chain of the anti-human…
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of the anti-human ROBO1 antibody B5209B Fab | protein | 211 | 6% helix, 51% strand | — |
| H | Heavy chain of the anti-human ROBO1 antibody B5209B Fab | protein | 214 | 7% helix, 53% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.61 | 0.75 | 54 | GOL |
| 2 | 67 | 0.50 | 0.85 | 23 | GOL |
| 3 | 118 | 0.37 | 0.74 | 20 | GOL |
| 4 | 63 | 0.31 | 0.75 | 15 | empty |
| 5 | 60 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- L–H · 1772 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6A76 · Crystal structure of the Fab fragment of B5209B, a murine monoclonal antibody specific… · 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 6A76 · PDBe 6A76
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