Research workbench
Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the scFv 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
- 6A78
- Type
- protein
- Length
- 641 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Homo sapiens; Mus musculus
- Molecule
- Roundabout homolog 1; Light chain region of the anti-human Robo1 antibody B5209B scFv…
- UniProt
- Q9Y6N7
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.1 · 5 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Roundabout homolog 1 | protein | 90 | 3% helix, 53% strand | Q9Y6N7 |
| L | Light chain region of the anti-human Robo1 antibody B5209B scFv | protein | 108 | 3% helix, 49% strand | — |
| H | Heavy chain and linker region of the anti-human Robo1 antibody B5209B scFv | protein | 121 | 5% helix, 50% strand | — |
| M | Light chain region of the anti-human Robo1 antibody B5209B scFv | protein | 110 | 3% helix, 48% strand | — |
| I | Heavy chain and linker region of the anti-human Robo1 antibody B5209B scFv | protein | 122 | 5% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains L, H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.78 | 0.81 | 73 | empty |
| 2 | 199 | 0.50 | 0.76 | 33 | empty |
| 3 | 190 | 0.49 | 0.76 | 33 | empty |
| 4 | 119 | 0.41 | 0.76 | 20 | empty |
| 5 | 118 | 0.41 | 0.75 | 19 | empty |
Interfaces
10 interfaces between chains.
- M–I · 917 Ų buried · 5 hydrogen bonds · protein-protein
- L–H · 901 Ų buried · 6 hydrogen bonds · protein-protein
- B–I · 467 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 460 Ų buried · 6 hydrogen bonds · protein-protein
- H–B · 373 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6A78 · Crystal structure of the fifth immunoglobulin domain (IG5) of human ROBO1 in complex with… · the same entry in another collection · chain H against H, 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 0.97
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 6A78 · PDBe 6A78 · UniProt Q9Y6N7
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