Research workbench
KRAS G12V, bound to gppnhp and miniprotein 225-15A/B
Analyse KRAS G12V, bound to gppnhp and miniprotein 225-15A/B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WLB
- Type
- protein
- Length
- 452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; 225-15 a; 225-15 B
- UniProt
- P01116
- Ligands
- GNP, MG, SO4
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 159 | 36% helix, 25% strand | P01116 |
| B | 225-15 a | protein | 34 | 53% helix, 0% strand | — |
| C | 225-15 B | protein | 34 | 53% helix, 0% strand | — |
| D | GTPase KRAS | protein | 163 | 35% helix, 25% strand | P01116 |
| E | 225-15 a | protein | 32 | 56% helix, 0% strand | — |
| F | 225-15 B | protein | 30 | 57% helix, 0% strand | — |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 2 copies · chains C
- PG4 · Tetraethylene glycol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.47 | 0.79 | 16 | empty |
| 2 | 128 | 0.46 | 0.78 | 21 | empty |
| 3 | 107 | 0.40 | 0.76 | 19 | empty |
| 4 | 72 | 0.35 | 0.76 | 17 | empty |
| 5 | 56 | 0.26 | 0.73 | 12 | PG4 |
Interfaces
7 interfaces between chains.
- D–E · 940 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 937 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 912 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 798 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 793 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5WLB · KRas G12V, bound to GppNHp and miniprotein 225-15a/b · 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 5WLB · PDBe 5WLB · UniProt P01116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.