Research workbench
Complex structure of the gap domain of mgcracgap and CDC42
Analyse Complex structure of the gap domain of mgcracgap and CDC42 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C2J
- Type
- protein
- Length
- 392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rac GTPase-activating protein 1; Cell division control protein 42 homolog
- UniProt
- Q9H0H5, P60766
- Ligands
- GDP, AF3, MG
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rac GTPase-activating protein 1 | protein | 201 | 62% helix, 1% strand | Q9H0H5 |
| B | Cell division control protein 42 homolog | protein | 191 | 40% helix, 23% strand | P60766 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A, B
- AF3 · Aluminum fluoride · ligand · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.72 | 0.79 | 61 | MG, GDP, AF3 |
| 2 | 280 | 0.61 | 0.80 | 42 | empty |
| 3 | 57 | 0.39 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1257 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5C2J · Complex structure of the GAP domain of MgcRacGAP and Cdc42 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H0H5 · AlphaFold monomer V2.0 prediction for rac GTPase-activating protein 1 (Q9H0H5) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P60766 · AlphaFold monomer V2.0 prediction for cell division control protein 42 homolog (P60766) · 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 Q9H0H5
- Every structure of UniProt P60766
- Elsewhere: RCSB PDB 5C2J · PDBe 5C2J · UniProt Q9H0H5 · UniProt P60766
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