MolNFT v1 · #138373 · protein
KRAS G12V, bound to GDP and miniprotein 225-11(A30R)
5WHB · GTPase KRAS: “KRAS G12V, bound to GDP and miniprotein 225-11(A30R)”. X-ray diffraction, 3 ligands (GDP, CA, MG), 6 pockets (best druggability 0.75). MolNFT v1 #138373 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WHB
- Type
- protein
- Length
- 875 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; RAS binder peptide: 225-11 (A30R)
- UniProt
- P01116
- Ligands
- GDP, CA, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 160 | 38% helix, 26% strand | P01116 |
| B, E | RAS binder peptide: 225-11 (A30R) | protein | 30 | 57% helix, 0% strand | — |
| C, F, I, L | RAS binder peptide: 225-11 (A30R) | protein | 31 | 58% helix, 0% strand | — |
| D | GTPase KRAS | protein | 158 | 38% helix, 26% strand | P01116 |
| G | GTPase KRAS | protein | 158 | 37% helix, 25% strand | P01116 |
| H, K | RAS binder peptide: 225-11 (A30R) | protein | 29 | 59% helix, 0% strand | — |
| J | GTPase KRAS | protein | 157 | 38% helix, 26% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, D, G, J
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, J, K, L
- 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.75 | 0.78 | 92 | CA |
| 2 | 868 | 0.73 | 0.78 | 65 | empty |
| 3 | 401 | 0.60 | 0.76 | 38 | GDP |
| 4 | 149 | 0.41 | 0.74 | 26 | empty |
| 5 | 93 | 0.40 | 0.77 | 18 | empty |
Interfaces
23 interfaces between chains.
- A–B · 855 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 850 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 848 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 848 Ų buried · 10 hydrogen bonds · protein-protein
- K–L · 733 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5WHB · KRas G12V, bound to GDP and miniprotein 225-11(A30R) · 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 5WHB · PDBe 5WHB · UniProt P01116
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