MolNFT v1 · #138372 · protein
KRAS G12V, bound to GDP and miniprotein 225-11
5WHA · GTPase KRAS: “KRAS G12V, bound to GDP and miniprotein 225-11”. X-ray diffraction, 3 ligands (GDP, CA, MG), 5 pockets (best druggability 0.69). MolNFT v1 #138372 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WHA
- Type
- protein
- Length
- 858 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Miniprotein 225-11
- UniProt
- P01116
- Ligands
- GDP, CA, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 7 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 153 | 39% helix, 27% strand | P01116 |
| B, F, H, I, L | Miniprotein 225-11 | protein | 30 | 57% helix, 0% strand | — |
| C | Miniprotein 225-11 | protein | 31 | 55% helix, 0% strand | — |
| D | GTPase KRAS | protein | 153 | 37% helix, 25% strand | P01116 |
| E, K | Miniprotein 225-11 | protein | 29 | 59% helix, 0% strand | — |
| G | GTPase KRAS | protein | 162 | 36% helix, 25% strand | P01116 |
| J | GTPase KRAS | protein | 151 | 38% helix, 27% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, D, G, J
- CA · Calcium ion · metal · 8 copies · chains A, B, D, E, G, H, L, I, J, K
- MG · Magnesium ion · metal · 4 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.69 | 0.77 | 79 | empty |
| 2 | 637 | 0.67 | 0.76 | 56 | empty |
| 3 | 374 | 0.57 | 0.75 | 38 | empty |
| 4 | 100 | 0.36 | 0.74 | 17 | empty |
| 5 | 52 | 0.35 | 0.79 | 13 | empty |
Interfaces
24 interfaces between chains.
- G–H · 910 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 833 Ų buried · 12 hydrogen bonds · protein-protein
- J–K · 803 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 795 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 746 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5WHA · KRas G12V, bound to GDP and miniprotein 225-11 · 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 5WHA · PDBe 5WHA · UniProt P01116
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