MolNFT v1 · #75881 · protein
Crystal structure of plexin A2 rbd in complex with RND1
3Q3J · Plexin-A2: “Crystal structure of plexin A2 rbd in complex with RND1”. X-ray diffraction, 3 ligands (GNP, MG, UNX), 1 pocket (best druggability 0.59). MolNFT v1 #75881 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3Q3J
- Type
- protein
- Length
- 277 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plexin-A2; Rho-related GTP-binding protein RHO6
- UniProt
- O75051, Q92730
- Ligands
- GNP, MG, UNX
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plexin-A2 | protein | 102 | 19% helix, 31% strand | O75051 |
| B | Rho-related GTP-binding protein RHO6 | protein | 175 | 43% helix, 24% strand | Q92730 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains B
- MG · Magnesium ion · metal · chains B
- UNX · Unknown atom or ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.59 | 0.82 | 34 | GNP, MG |
Interfaces
1 interface between chains.
- A–B · 662 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3Q3J · Crystal structure of plexin A2 RBD in complex with Rnd1 · 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
- O75051 · AlphaFold monomer V2.0 prediction for plexin-A2 (O75051) · 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 O75051
- Every structure of UniProt Q92730
- Elsewhere: RCSB PDB 3Q3J · PDBe 3Q3J · UniProt O75051 · UniProt Q92730
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