MolNFT v1 · #79129 · protein
Crystal structure of a truncated intracellular domain of plexin-B1 in complex with RAC1
3SU8 · RAS-related C3 botulinum toxin substrate 1: “Crystal structure of a truncated intracellular domain of plexin-B1 in complex with RAC1”. X-ray diffraction, 2 ligands (GNP, MG), 10 pockets (best druggability 0.65). MolNFT v1 #79129 on…
- PDB
- 3SU8
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related C3 botulinum toxin substrate 1; Plexin-B1
- UniProt
- P63000, O43157
- Ligands
- GNP, MG
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related C3 botulinum toxin substrate 1 | protein | 178 | 37% helix, 24% strand | P63000 |
| X | Plexin-B1 | protein | 539 | 54% helix, 8% strand | O43157 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.65 | 0.84 | 31 | empty |
| 2 | 143 | 0.56 | 0.82 | 33 | MG, GNP |
| 3 | 189 | 0.50 | 0.76 | 28 | empty |
| 4 | 185 | 0.49 | 0.77 | 27 | empty |
| 5 | 54 | 0.41 | 0.82 | 14 | empty |
Interfaces
1 interface between chains.
- A–X · 731 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3SU8 · Crystal structure of a truncated intracellular domain of Plexin-B1 in complex with Rac1 · the same entry in another collection · chain A against A, TM-score 1.00
- O43157 · AlphaFold monomer V2.0 prediction for plexin-B1 (O43157) · a predicted model of the same protein · chain X against A, TM-score 0.94
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 P63000
- Every structure of UniProt O43157
- Elsewhere: RCSB PDB 3SU8 · PDBe 3SU8 · UniProt P63000 · UniProt O43157
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