MolNFT v1 · #138376 · protein
KRAS G12V/D38P, bound to gppnhp and miniprotein 225-11
5WHE · GTPase KRAS: “KRAS G12V/D38P, bound to gppnhp and miniprotein 225-11”. X-ray diffraction, 3 ligands (GNP, CA, MG), 8 pockets (best druggability 0.74). MolNFT v1 #138376 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WHE
- Type
- protein
- Length
- 875 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Miniprotein 225-11
- UniProt
- P01116
- Ligands
- GNP, CA, MG
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 163 | 37% helix, 24% strand | P01116 |
| D | GTPase KRAS | protein | 157 | 38% helix, 25% strand | P01116 |
| G | GTPase KRAS | protein | 154 | 38% helix, 25% strand | P01116 |
| J | GTPase KRAS | protein | 157 | 38% helix, 25% strand | P01116 |
| B, E, H, L | Miniprotein 225-11 | protein | 30 | 60% helix, 0% strand | — |
| C, F, I, K | Miniprotein 225-11 | protein | 31 | 55% helix, 0% strand | — |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, J, D, G
- CA · Calcium ion · metal · 10 copies · chains A, B, D, E, G, H, F
- 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.74 | 0.77 | 105 | GNP, MG |
| 2 | 502 | 0.67 | 0.78 | 50 | empty |
| 3 | 444 | 0.65 | 0.78 | 44 | empty |
| 4 | 100 | 0.58 | 0.86 | 22 | empty |
| 5 | 76 | 0.58 | 0.88 | 24 | empty |
Interfaces
23 interfaces between chains.
- A–B · 893 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 838 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 831 Ų buried · 12 hydrogen bonds · protein-protein
- J–K · 811 Ų buried · 12 hydrogen bonds · protein-protein
- H–I · 722 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5WHE · KRas G12V/D38P, bound to GppNHp and miniprotein 225-11 · the same entry in another collection · chain H against H, 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 5WHE · PDBe 5WHE · UniProt P01116
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