Research workbench
Crystal structure of human KRAS G12D mutant in complex with GDP
Analyse Crystal structure of human KRAS G12D 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
- 5US4
- Type
- protein
- Length
- 326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, MG
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 164 | 38% helix, 26% strand | P01116 |
| B | GTPase KRAS | protein | 162 | 37% helix, 26% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · 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 | 132 | 0.49 | 0.79 | 25 | GDP, MG |
| 2 | 122 | 0.47 | 0.79 | 25 | GDP, MG |
| 3 | 114 | 0.42 | 0.77 | 24 | empty |
| 4 | 124 | 0.38 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1051 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5US4 · Crystal structure of human KRAS G12D 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 5US4 · PDBe 5US4 · UniProt P01116
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