MolNFT v1 · #104078 · protein
Second-site screening of K-RAS in the presence of covalently attached first-site ligands
4PZY: “Second-site screening of K-RAS in the presence of covalently attached first-site ligands”. X-ray diffraction, 3 ligands (GDP, 2XR, MG), 5 pockets (best druggability 0.71). MolNFT v1 #104078 on GenesisL1: 3D structure, binding sites…
- PDB
- 4PZY
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K-RAS
- EC
- 3.6.5.2
- UniProt
- P01116
- Ligands
- GDP, 2XR, MG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | K-RAS (EC 3.6.5.2) | protein | 170 | 37% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- 2XR · 2-chloro-1-(1H-indol-3-yl)ethanone · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.71 | 0.82 | 43 | empty |
| 2 | 229 | 0.68 | 0.85 | 38 | 2XR |
| 3 | 228 | 0.58 | 0.79 | 42 | GDP, MG |
| 4 | 145 | 0.50 | 0.79 | 27 | GDP, MG |
| 5 | 65 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 699 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4PZY · Second-site screening of K-Ras in the presence of covalently attached first-site ligands · 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 4PZY · PDBe 4PZY · UniProt P01116
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