Research workbench
Crystal structure of the effector domain of PLXNB1 bound with RND1 GTPase
Analyse Crystal structure of the effector domain of PLXNB1 bound with RND1 GTPase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2REX
- Type
- protein
- Length
- 565 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-B1; Rho-related GTP-binding protein RHO6
- UniProt
- O43157, Q92730
- Ligands
- GNP, MG, CA, UNX
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Plexin-B1 | protein | 107 | 21% helix, 36% strand | O43157 |
| B | Rho-related GTP-binding protein RHO6 | protein | 171 | 40% helix, 24% strand | Q92730 |
| D | Rho-related GTP-binding protein RHO6 | protein | 180 | 37% helix, 25% strand | Q92730 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- CA · Calcium ion · metal · 2 copies · chains B, D
- UNX · Unknown atom or ion · ion · 30 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.59 | 0.82 | 33 | MG, GNP, UNX |
| 2 | 155 | 0.58 | 0.82 | 29 | MG, GNP |
| 3 | 70 | 0.29 | 0.73 | 16 | UNX |
Interfaces
3 interfaces between chains.
- A–B · 693 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 690 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2REX · Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase · the same entry in another collection · chain A against A, TM-score 1.00
- Q92730 · AlphaFold monomer V2.0 prediction for rho-related GTP-binding protein RHO6 (Q92730) · a predicted model of the same protein · chain B against A, TM-score 0.99
- O43157 · AlphaFold monomer V2.0 prediction for plexin-B1 (O43157) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 O43157
- Every structure of UniProt Q92730
- Elsewhere: RCSB PDB 2REX · PDBe 2REX · UniProt O43157 · UniProt Q92730
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