MolNFT v1 · #158773 · protein
Crystal structure of human KRAS P34R mutant in complex with gnp and phosphate
6O46 · GTPase KRAS: “Crystal structure of human KRAS P34R mutant in complex with gnp and phosphate”. X-ray diffraction, 3 ligands (GNP, MG, PO4), 4 pockets (best druggability 0.70). MolNFT v1 #158773 on GenesisL1: 3D structure, binding…
- PDB
- 6O46
- Type
- protein
- Length
- 505 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- EC
- 3.-.-.-
- UniProt
- P01116
- Ligands
- GNP, MG, PO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS (EC 3.-.-.-) | protein | 169 | 36% helix, 25% strand | P01116 |
| B, C | GTPase KRAS (EC 3.-.-.-) | protein | 168 | 38% helix, 24% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.70 | 0.79 | 72 | GNP, MG |
| 2 | 255 | 0.58 | 0.79 | 28 | GNP, MG |
| 3 | 125 | 0.48 | 0.79 | 25 | empty |
| 4 | 135 | 0.45 | 0.77 | 33 | GNP, MG |
Interfaces
3 interfaces between chains.
- A–C · 393 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 346 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 318 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6O46 · Crystal structure of human KRAS P34R mutant in complex with GNP and Phosphate · 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 6O46 · PDBe 6O46 · UniProt P01116
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