MolNFT v1 · #179694 · protein
The complex between rhod and the plexin B2 rbd
7KDC · Rho-related GTP-binding protein rhod: “The complex between rhod and the plexin B2 rbd”. X-ray diffraction, 2 ligands (GNP, MG), 2 pockets (best druggability 0.55). MolNFT v1 #179694 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7KDC
- Type
- protein
- Length
- 566 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho-related GTP-binding protein rhod; Plexin-B2
- UniProt
- O00212, B2RXS4
- Ligands
- GNP, MG
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rho-related GTP-binding protein rhod | protein | 180 | 42% helix, 26% strand | O00212 |
| C, D | Plexin-B2 | protein | 103 | 15% helix, 28% strand | B2RXS4 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.55 | 0.82 | 31 | GNP, MG |
| 2 | 130 | 0.53 | 0.81 | 30 | GNP, MG |
Interfaces
3 interfaces between chains.
- C–D · 2358 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 715 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 707 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7KDC · The complex between RhoD and the Plexin B2 RBD · the same entry in another collection · chain A against A, TM-score 1.00
- O00212 · AlphaFold monomer V2.0 prediction for rho-related GTP-binding protein rhod (O00212) · a predicted model of the same protein · chain A against A, TM-score 0.99
- B2RXS4 · AlphaFold monomer V2.0 prediction for plexin-B2 (B2RXS4) · a predicted model of the same protein · chain C against A, TM-score 0.54
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 O00212
- Every structure of UniProt B2RXS4
- Elsewhere: RCSB PDB 7KDC · PDBe 7KDC · UniProt O00212 · UniProt B2RXS4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.