Research workbench
Crystal structure of human KRAS G12A mutant in complex with gppnhp
Analyse Crystal structure of human KRAS G12A mutant in complex with gppnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VPY
- Type
- protein
- Length
- 312 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- 9GM, MG
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTPase KRAS | protein | 156 | 33% helix, 26% strand | P01116 |
Ligands and binding sites
- 9GM · 2-amino-9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-alpha-L-xylofuranosyl}-1,9-dihydro-6H-purin-6-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
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 | 179 | 0.47 | 0.76 | 30 | PG4 |
| 2 | 84 | 0.36 | 0.76 | 24 | empty |
| 3 | 100 | 0.35 | 0.74 | 22 | MG, 9GM |
| 4 | 84 | 0.34 | 0.75 | 24 | MG, 9GM |
Interfaces
1 interface between chains.
- A–B · 1064 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5VPY · Crystal structure of human KRAS G12A mutant in complex with GppNHp · 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 5VPY · PDBe 5VPY · UniProt P01116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.