Research workbench
Crystal structure of human KRAS P34R mutant in complex with gnp and phosphate
Analyse Crystal structure of human KRAS P34R mutant in complex with gnp and phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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