Research workbench
Crystal structure of human KRAS P34R mutant in complex with GNP
Analyse Crystal structure of human KRAS P34R mutant in complex with GNP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O36
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- GTPase KRas
- EC
- 3.-.-.-
- UniProt
- P01116
- Ligands
- GNP, MG, PO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | GTPase KRas (EC 3.-.-.-) | protein | 168 | 33% helix, 25% 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.70 | 0.78 | 71 | MG, GNP |
| 2 | 176 | 0.50 | 0.77 | 27 | MG, GNP |
| 3 | 125 | 0.46 | 0.78 | 19 | empty |
| 4 | 90 | 0.40 | 0.78 | 24 | MG, GNP |
Interfaces
3 interfaces between chains.
- A–C · 432 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 311 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6O36 · Crystal structure of human KRAS P34R mutant in complex with gnp · 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 6O36 · PDBe 6O36 · UniProt P01116
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