MolNFT v1 · #143861 · protein
A complex between pH domain of P190RHOGEF and activated RAC1 bound to a GTP analog
6BC1 · RAS-related C3 botulinum toxin substrate 1: “A complex between pH domain of P190RHOGEF and activated RAC1 bound to a GTP analog”. X-ray diffraction, 2 ligands (GSP, MG), 8 pockets (best druggability 0.65). MolNFT v1 #143861 on…
- PDB
- 6BC1
- Type
- protein
- Length
- 636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related C3 botulinum toxin substrate 1; Rho guanine nucleotide exchange factor 28
- UniProt
- P63000, Q8N1W1
- Ligands
- GSP, MG
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related C3 botulinum toxin substrate 1 | protein | 177 | 38% helix, 26% strand | P63000 |
| C, D | Rho guanine nucleotide exchange factor 28 | protein | 141 | 22% helix, 42% strand | Q8N1W1 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.65 | 0.78 | 44 | empty |
| 2 | 308 | 0.60 | 0.78 | 32 | empty |
| 3 | 344 | 0.59 | 0.76 | 33 | empty |
| 4 | 125 | 0.54 | 0.82 | 31 | GSP, MG |
| 5 | 108 | 0.49 | 0.81 | 27 | GSP |
Interfaces
3 interfaces between chains.
- C–D · 759 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 506 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 505 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6BC1 · A Complex between PH Domain of p190RhoGEF and Activated Rac1 Bound to a GTP Analog · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N1W1 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 28 (Q8N1W1) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P63000
- Every structure of UniProt Q8N1W1
- Elsewhere: RCSB PDB 6BC1 · PDBe 6BC1 · UniProt P63000 · UniProt Q8N1W1
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