Research workbench
Transition state complex for GTP hydrolysis by CDC42: comparisons of the high resolution structures for CDC42 bound to the active and catalytically compromised forms of the CDC42-gap.
Analyse Transition state complex for GTP hydrolysis by CDC42: comparisons of the high… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NGR
- Type
- protein
- Length
- 387 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (GTP binding protein (G25K)); Protein (GTPase activating protein (rhg))
- UniProt
- P60953, Q07960
- Ligands
- GDP, AF3, MG
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (GTP binding protein (G25K)) | protein | 191 | 37% helix, 24% strand | P60953 |
| B | Protein (GTPase activating protein (rhg)) | protein | 196 | 64% helix, 0% strand | Q07960 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- AF3 · Aluminum fluoride · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.70 | 0.78 | 64 | MG, GDP, AF3 |
| 2 | 92 | 0.46 | 0.80 | 22 | empty |
| 3 | 120 | 0.42 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1116 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2NGR · Transition state complex for GTP hydrolysis by CDC42: comparisons of the high resolution… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07960 · AlphaFold monomer V2.0 prediction for rho GTPase-activating protein 1 (Q07960) · 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 A 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
- Every structure of UniProt Q07960
- Elsewhere: RCSB PDB 2NGR · PDBe 2NGR · UniProt P60953 · UniProt Q07960
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