Research workbench
G12V mutant of human placental CDC42 GTPase in the GDP form
Analyse G12V mutant of human placental CDC42 GTPase in the GDP form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1A4R
- Type
- protein
- Length
- 380 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G25K GTP-binding protein
- UniProt
- P60953
- Ligands
- GDP, GNH, MG
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | G25K GTP-binding protein | protein | 190 | 39% helix, 22% strand | P60953 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- GNH · Aminophosphonic acid-guanylate ester · ligand · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.59 | 0.75 | 46 | empty |
| 2 | 214 | 0.50 | 0.76 | 29 | empty |
| 3 | 101 | 0.42 | 0.77 | 28 | MG, GDP |
| 4 | 68 | 0.33 | 0.76 | 12 | empty |
| 5 | 77 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 560 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1A4R · G12V mutant of human placental CDC42 GTPase in the GDP form · 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 0.91
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 1A4R · PDBe 1A4R · UniProt P60953
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