MolNFT v1 · #134644 · protein
Crystal structure of farnesylated and methylated KRAS4B in complex with pde-delta (crystal form II - with ordered hypervariable region)
5TAR · GTPase KRAS: “Crystal structure of farnesylated and methylated KRAS4B in complex with pde-delta (crystal form II - with…”. X-ray diffraction, 2 ligands (FAR, GDP), 2 pockets (best druggability 0.83). MolNFT v1 #134644 on GenesisL1…
- PDB
- 5TAR
- Type
- protein
- Length
- 333 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit…
- UniProt
- P01116, O43924
- Ligands
- FAR, GDP
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 185 | 43% helix, 22% strand | P01116 |
| B | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta | protein | 148 | 16% helix, 59% strand | O43924 |
Ligands and binding sites
- FAR · Farnesyl · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.83 | 0.96 | 28 | FAR |
| 2 | 71 | 0.34 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 504 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid, 1 modified (farnesylation, nonstandard).
Compared structures
- 5TAR · Crystal structure of farnesylated and methylated kras4b in complex with PDE-delta… · the same entry in another collection · chain A against A, TM-score 1.00
- O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.97
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
- Every structure of UniProt O43924
- Elsewhere: RCSB PDB 5TAR · PDBe 5TAR · UniProt P01116 · UniProt O43924
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.