MolNFT v1 · #142536 · protein
Crystal structure of the fifth immunoglobulin domain (IG5) of human ROBO1 in complex with the mutant scfv fragment (P103A) of murine monoclonal antibody B5209B
6A79 · Roundabout homolog 1: “Crystal structure of the fifth immunoglobulin domain (IG5) of human ROBO1 in complex with the mutant scfv…”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.78). MolNFT v1 #142536 on…
- PDB
- 6A79
- 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
- 6 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 3% 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, I | Heavy chain of the anti-human ROBO1 antibody B5209B scfv | protein | 122 | 5% helix, 49% strand | — |
| M | Light chain region of the anti-human ROBO1 antibody B5209B scfv | protein | 109 | 3% 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.78 | 0.80 | 96 | empty |
| 2 | 355 | 0.58 | 0.76 | 47 | empty |
| 3 | 213 | 0.50 | 0.76 | 32 | empty |
| 4 | 137 | 0.41 | 0.74 | 25 | empty |
| 5 | 105 | 0.38 | 0.75 | 16 | empty |
Interfaces
10 interfaces between chains.
- M–I · 901 Ų buried · 6 hydrogen bonds · protein-protein
- L–H · 875 Ų buried · 6 hydrogen bonds · protein-protein
- B–I · 473 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 463 Ų buried · 6 hydrogen bonds · protein-protein
- B–M · 340 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6A79 · Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with… · the same entry in another collection · chain M against M, 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 6A79 · PDBe 6A79 · UniProt Q9Y6N7
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