MolNFT v1 · #138375 · protein
Crystal structure of KRAS G12V/D38P, bound to GDP
5WHD · GTPase KRAS: “Crystal structure of KRAS G12V/D38P, bound to GDP”. X-ray diffraction, 1 ligand (GDP), 3 pockets (best druggability 0.54). MolNFT v1 #138375 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WHD
- Type
- protein
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 165 | 39% helix, 23% strand | P01116 |
| B | GTPase KRAS | protein | 162 | 39% helix, 24% strand | P01116 |
| C | GTPase KRAS | protein | 157 | 39% helix, 25% strand | P01116 |
| D | GTPase KRAS | protein | 155 | 39% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.54 | 0.76 | 31 | empty |
| 2 | 85 | 0.36 | 0.76 | 18 | empty |
| 3 | 61 | 0.33 | 0.77 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–D · 885 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 279 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 221 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 186 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5WHD · Crystal structure of KRas G12V/D38P, bound to GDP · the same entry in another collection · chain D against D, 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 5WHD · PDBe 5WHD · UniProt P01116
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