Research workbench
Crystal structure of the intracellular domain of plexin-B1 in complex with RAC1
Analyse Crystal structure of the intracellular domain of plexin-B1 in complex with RAC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SUA
- Type
- protein
- Length
- 2,048 residues
- Chains
- 6
- 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
- 17 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | RAS-related C3 botulinum toxin substrate 1 | protein | 178 | 40% helix, 19% strand | P63000 |
| D | Plexin-B1 | protein | 503 | 57% helix, 9% strand | O43157 |
| E | Plexin-B1 | protein | 505 | 56% helix, 9% strand | O43157 |
| F | Plexin-B1 | protein | 506 | 56% helix, 9% strand | O43157 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.71 | 0.77 | 87 | MG, GNP |
| 2 | 710 | 0.70 | 0.77 | 82 | MG, GNP |
| 3 | 697 | 0.69 | 0.77 | 89 | MG, GNP |
| 4 | 385 | 0.66 | 0.80 | 36 | empty |
| 5 | 366 | 0.66 | 0.80 | 36 | empty |
Interfaces
9 interfaces between chains.
- B–E · 741 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 728 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 717 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 579 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 570 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3SUA · Crystal structure of the intracellular domain of Plexin-B1 in complex with Rac1 · the same entry in another collection · chain F against F, TM-score 1.00
- O43157 · AlphaFold monomer V2.0 prediction for plexin-B1 (O43157) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 3SUA · PDBe 3SUA · UniProt P63000 · UniProt O43157
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