Research workbench
CDC42 bound to gmp-pcp: induced fit by effector is required
Analyse CDC42 bound to gmp-pcp: induced fit by effector is required in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QRZ
- Type
- protein
- Length
- 375 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 42 homolog precursor
- UniProt
- P60953
- Ligands
- GCP, MG, SO4
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division control protein 42 homolog precursor | protein | 189 | 38% helix, 22% strand | P60953 |
| B | Cell division control protein 42 homolog precursor | protein | 186 | 32% helix, 22% strand | P60953 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.56 | 0.77 | 35 | empty |
| 2 | 365 | 0.55 | 0.74 | 46 | SO4 |
| 3 | 95 | 0.37 | 0.75 | 18 | MG, GCP |
| 4 | 55 | 0.27 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 616 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2QRZ · Cdc42 bound to GMP-PCP: Induced Fit by Effector is Required · the same entry in another collection · chain A against A, TM-score 1.00
- P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P60953
- Elsewhere: RCSB PDB 2QRZ · PDBe 2QRZ · UniProt P60953
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