Research workbench
Crystal structure of the fifth immunoglobulin domain (IG5) of human ROBO1 in complex with the Fab fragment of murine monoclonal antibody B5209B
Analyse Crystal structure of the fifth immunoglobulin domain (IG5) of human ROBO1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A77
- Type
- protein
- Length
- 519 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roundabout homolog 1; Light chain of the anti-human ROBO1 antibody B5209B Fab; Heavy…
- UniProt
- Q9Y6N7
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Roundabout homolog 1 | protein | 91 | 3% helix, 54% strand | Q9Y6N7 |
| L | Light chain of the anti-human ROBO1 antibody B5209B Fab | protein | 211 | 6% helix, 55% strand | — |
| H | Heavy chain of the anti-human ROBO1 antibody B5209B Fab | protein | 217 | 8% helix, 53% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.72 | 0.77 | 71 | empty |
| 2 | 134 | 0.49 | 0.79 | 20 | empty |
| 3 | 113 | 0.42 | 0.77 | 27 | empty |
| 4 | 96 | 0.38 | 0.76 | 23 | empty |
| 5 | 71 | 0.32 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1823 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 495 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 402 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6A77 · Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y6N7 · AlphaFold monomer V2.0 prediction for roundabout homolog 1 (Q9Y6N7) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9Y6N7
- Elsewhere: RCSB PDB 6A77 · PDBe 6A77 · UniProt Q9Y6N7
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