Research workbench
Crystal structure of the third fibronectin domain (FN3) of human ROBO1 in complex with the Fab fragment of murine monoclonal antibody B2212A.
Analyse Crystal structure of the third fibronectin domain (FN3) 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
- 3WIH
- Type
- protein
- Length
- 1,040 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roundabout homolog 1; Anti-human ROBO1 antibody B2212A Fab light chain; Anti-human ROBO1…
- UniProt
- Q9Y6N7
- Pockets
- 16 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Roundabout homolog 1 | protein | 88 | 3% helix, 45% strand | Q9Y6N7 |
| L, M | Anti-human ROBO1 antibody B2212A Fab light chain | protein | 213 | 5% helix, 50% strand | — |
| H, I | Anti-human ROBO1 antibody B2212A Fab heavy chain | protein | 219 | 8% helix, 52% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.68 | 0.81 | 48 | empty |
| 2 | 260 | 0.51 | 0.75 | 39 | empty |
| 3 | 228 | 0.50 | 0.75 | 37 | empty |
| 4 | 244 | 0.49 | 0.74 | 38 | GOL |
| 5 | 213 | 0.47 | 0.74 | 37 | empty |
Interfaces
9 interfaces between chains.
- L–H · 1945 Ų buried · 17 hydrogen bonds · protein-protein
- M–I · 1927 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 544 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 543 Ų buried · 9 hydrogen bonds · protein-protein
- B–M · 414 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3WIH · Crystal structure of the third fibronectin domain (Fn3) 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 0.95
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 3WIH · PDBe 3WIH · UniProt Q9Y6N7
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