Research workbench
The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)
Analyse The crystal structure of human cdc42 in complex with the CRIB domain of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ODB
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Human Cell Division Cycle 42 (CDC42); Serine/threonine-protein kinase PAK 6
- UniProt
- P60953, Q9NQU5
- Ligands
- GCP, MG, SO4, CL
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human Cell Division Cycle 42 (CDC42) | protein | 177 | 40% helix, 24% strand | P60953 |
| B | Serine/threonine-protein kinase PAK 6 | protein | 35 | 20% helix, 46% strand | Q9NQU5 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.54 | 0.79 | 39 | MG, GCP |
Interfaces
1 interface between chains.
- A–B · 1069 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2ODB · The crystal structure of human CDC42 in complex with the crib domain of human… · 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 A against A, TM-score 0.99
- Q9NQU5 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 6 (Q9NQU5) · a predicted model of the same protein · chain B against A, TM-score 0.59
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
- Every structure of UniProt Q9NQU5
- Elsewhere: RCSB PDB 2ODB · PDBe 2ODB · UniProt P60953 · UniProt Q9NQU5
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