Research workbench
KRAS G12V, bound to gppnhp and miniprotein 225-11
Analyse KRAS G12V, bound to gppnhp and miniprotein 225-11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WPL
- Type
- protein
- Length
- 871 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS; RAS-binding peptide
- UniProt
- P01112
- Ligands
- GNP, CA, MG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS | protein | 165 | 36% helix, 24% strand | P01112 |
| B, E, H, K | RAS-binding peptide | protein | 29 | 59% helix, 0% strand | — |
| C, F, L | RAS-binding peptide | protein | 31 | 58% helix, 0% strand | — |
| D, J | GTPase HRAS | protein | 156 | 38% helix, 26% strand | P01112 |
| G | GTPase HRAS | protein | 153 | 39% helix, 25% strand | P01112 |
| I | RAS-binding peptide | protein | 32 | 56% helix, 0% strand | — |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, J, D, G
- CA · Calcium ion · metal · 8 copies · chains A, B, D, E, G, H, J, K, L
- MG · Magnesium ion · metal · 5 copies · chains A, D, G, H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.75 | 0.79 | 86 | GNP, MG |
| 2 | 440 | 0.65 | 0.78 | 46 | empty |
| 3 | 345 | 0.64 | 0.79 | 33 | empty |
| 4 | 96 | 0.60 | 0.87 | 22 | empty |
| 5 | 76 | 0.59 | 0.89 | 20 | empty |
Interfaces
22 interfaces between chains.
- A–B · 920 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 830 Ų buried · 12 hydrogen bonds · protein-protein
- J–K · 820 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 818 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 711 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5WPL · KRas G12V, bound to GppNHp 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 P01112
- Elsewhere: RCSB PDB 5WPL · PDBe 5WPL · UniProt P01112
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