MolNFT v1 · #52510 · protein
Complex of RAC2 and PLCG2 spph domain
2W2X · RAS-related C3 botulinum toxin substrate 2: “Complex of RAC2 and PLCG2 spph domain”. X-ray diffraction, 2 ligands (GSP, MG), 6 pockets (best druggability 0.68). MolNFT v1 #52510 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2W2X
- Type
- protein
- Length
- 561 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related C3 botulinum toxin substrate 2; 1-phosphatidylinositol-4,5-bisphosphate…
- EC
- 3.1.4.11
- UniProt
- P15153, P16885
- Ligands
- GSP, MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related C3 botulinum toxin substrate 2 | protein | 177 | 36% helix, 23% strand | P15153 |
| B | RAS-related C3 botulinum toxin substrate 2 | protein | 170 | 36% helix, 22% strand | P15153 |
| C | 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2 (EC 3.1.4.11) | protein | 109 | 17% helix, 41% strand | P16885 |
| D | 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2 (EC 3.1.4.11) | protein | 105 | 22% helix, 46% strand | P16885 |
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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.68 | 0.74 | 70 | empty |
| 2 | 215 | 0.61 | 0.81 | 44 | GSP, MG |
| 3 | 137 | 0.55 | 0.82 | 33 | GSP, MG |
| 4 | 84 | 0.34 | 0.75 | 22 | empty |
| 5 | 77 | 0.34 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–C · 573 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 492 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 160 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2W2X · Complex of Rac2 and PLCg2 spPH Domain · the same entry in another collection · chain D against D, TM-score 1.00
- P15153 · AlphaFold monomer V2.0 prediction for RAS-related C3 botulinum toxin substrate 2 (P15153) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P16885 · AlphaFold monomer V2.0 prediction for 1-phosphatidylinositol 4,5-bisphosphate… · a predicted model of the same protein · chain D 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 P15153
- Every structure of UniProt P16885
- Elsewhere: RCSB PDB 2W2X · PDBe 2W2X · UniProt P15153 · UniProt P16885
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