MolNFT v1 · #50321 · protein
Crystal structure of the effector domain of PLXNB1 bound with RND1 GTPase
2REX · Plexin-B1: “Crystal structure of the effector domain of PLXNB1 bound with RND1 GTPase”. X-ray diffraction, 4 ligands (GNP, MG, CA), 3 pockets (best druggability 0.59). MolNFT v1 #50321 on GenesisL1: 3D structure, binding sites and…
- 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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