MolNFT v1 · #142535 · protein
Crystal structure of the fifth immunoglobulin domain (IG5) of human ROBO1 in complex with the scfv fragment of murine monoclonal antibody B5209B
6A78 · Roundabout homolog 1: “Crystal structure of the fifth immunoglobulin domain (IG5) of human ROBO1 in complex with the scfv fragment…”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.78). MolNFT v1 #142535 on…
- PDB
- 6A78
- Type
- protein
- Length
- 641 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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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