MolNFT v1 · #50382 · protein
Crystal structure of P63RHOGEF complex with galpha-Q and rhoa
2RGN · Guanine nucleotide-binding protein G(I) subunit alpha-1…: “Crystal structure of P63RHOGEF complex with galpha-Q and rhoa”. X-ray diffraction, 3 ligands (ALF, GDP, MG), 20 pockets (best druggability 0.78). MolNFT v1 #50382 on…
- PDB
- 2RGN
- Type
- protein
- Length
- 1,646 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1, guanine nucleotide-binding…
- UniProt
- P10824, Q86VW2, P61586
- Ligands
- ALF, GDP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Guanine nucleotide-binding protein G(I) subunit alpha-1, guanine nucleotide-binding protein G(Q) subunit alpha | protein | 324 | 48% helix, 13% strand | P10824 |
| B | Rho guanine nucleotide exchange factor 25 | protein | 327 | 60% helix, 16% strand | Q86VW2 |
| C | Transforming protein rhoa | protein | 177 | 37% helix, 19% strand | P61586 |
| E | Rho guanine nucleotide exchange factor 25 | protein | 326 | 61% helix, 16% strand | Q86VW2 |
| F | Transforming protein rhoa | protein | 168 | 39% helix, 15% strand | P61586 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.78 | 0.80 | 107 | empty |
| 2 | 878 | 0.74 | 0.78 | 96 | empty |
| 3 | 352 | 0.73 | 0.85 | 30 | empty |
| 4 | 406 | 0.72 | 0.83 | 52 | ALF, MG, GDP |
| 5 | 254 | 0.69 | 0.85 | 38 | ALF, MG, GDP |
Interfaces
5 interfaces between chains.
- D–E · 1907 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1885 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1491 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1465 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 394 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2RGN · Crystal Structure of p63RhoGEF complex with Galpha-q and RhoA · the same entry in another collection · chain F against F, TM-score 1.00
- Q86VW2 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 25 (Q86VW2) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P10824 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P10824
- Every structure of UniProt Q86VW2
- Every structure of UniProt P61586
- Elsewhere: RCSB PDB 2RGN · PDBe 2RGN · UniProt P10824 · UniProt Q86VW2 · UniProt P61586
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