Research workbench
Drosophila robo IG1-2 (monoclinic form)
Analyse Drosophila robo IG1-2 (monoclinic form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VRA
- Type
- protein
- Length
- 781 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roundabout 1
- UniProt
- O44924
- Ligands
- SGN, IDS, SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Roundabout 1 | protein | 202 | 2% helix, 47% strand | O44924 |
| B | Roundabout 1 | protein | 201 | 5% helix, 43% strand | O44924 |
| C | Roundabout 1 | protein | 191 | 0% helix, 46% strand | O44924 |
| D | Roundabout 1 | protein | 187 | 0% helix, 44% strand | O44924 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 11 copies · chains A, C, B, D
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 | 927 | 0.74 | 0.78 | 103 | empty |
| 2 | 748 | 0.68 | 0.75 | 57 | empty |
| 3 | 639 | 0.64 | 0.74 | 63 | SO4 |
| 4 | 99 | 0.47 | 0.80 | 15 | SO4 |
| 5 | 98 | 0.45 | 0.80 | 16 | SO4 |
Interfaces
5 interfaces between chains.
- A–C · 523 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 492 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 482 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 438 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2VRA · Drosophila Robo IG1-2 (monoclinic form) · the same entry in another collection · chain A against A, TM-score 1.00
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 O44924
- Elsewhere: RCSB PDB 2VRA · PDBe 2VRA · UniProt O44924
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