Research workbench
Crystal structure of human KRAS G12A mutant in complex with GDP
Analyse Crystal structure of human KRAS G12A mutant in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VP7
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, MG, NA
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | GTPase KRAS | protein | 170 | 36% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, F
- MG · Magnesium ion · metal · 2 copies · chains A, F
- NA · Sodium ion · metal · 2 copies · chains A, F
- PGE · Triethylene glycol · additive · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.50 | 0.79 | 32 | GDP, MG |
| 2 | 163 | 0.50 | 0.78 | 33 | GDP, MG |
| 3 | 165 | 0.44 | 0.75 | 33 | PGE |
| 4 | 71 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–F · 1038 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5VP7 · Crystal structure of human KRAS G12A mutant in complex with GDP · the same entry in another collection · chain A against A, TM-score 1.00
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 P01116
- Elsewhere: RCSB PDB 5VP7 · PDBe 5VP7 · UniProt P01116
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