Research workbench
CDC42 binds PAK4 via an extended GTPase-effector interface - 3 peptide: PAK4CAT, PAK4-N45, CDC42
Analyse CDC42 binds PAK4 via an extended GTPase-effector interface - 3 peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UPK
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pak 4; Cell division control protein 42 homolog
- EC
- 2.7.11.1
- UniProt
- O96013, P60953
- Ligands
- ANP, GNP, MG
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 4 (EC 2.7.11.1) | protein | 40 | 8% helix, 35% strand | O96013 |
| B | SERINE/THREONINE-protein kinase pak 4 (EC 2.7.11.1) | protein | 289 | 44% helix, 18% strand | O96013 |
| C | Cell division control protein 42 homolog | protein | 175 | 42% helix, 25% strand | P60953 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains B
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains C
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.68 | 0.82 | 34 | ANP |
| 2 | 462 | 0.66 | 0.78 | 59 | empty |
| 3 | 196 | 0.56 | 0.80 | 39 | GNP, MG |
| 4 | 91 | 0.40 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1244 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 637 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 439 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5UPK · CDC42 binds PAK4 via an extended GTPase-effector interface - 3 peptide: PAK4cat… · the same entry in another collection · chain A against A, TM-score 1.00
- O96013 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 4 (O96013) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P60953 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60953) · 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 O96013
- Every structure of UniProt P60953
- Elsewhere: RCSB PDB 5UPK · PDBe 5UPK · UniProt O96013 · UniProt P60953
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