Research workbench
Second-site screening of K-RAS in the presence of covalently attached first-site ligands
Analyse Second-site screening of K-RAS in the presence of covalently attached… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q01
- Type
- protein
- Length
- 334 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, 2XH, MG
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | K-RAS (EC 3.6.5.2) | protein | 166 | 39% helix, 25% strand | P01116 |
| B | K-RAS (EC 3.6.5.2) | protein | 168 | 39% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- 2XH · naphthalene-1-thiol · 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
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 | 202 | 0.65 | 0.84 | 31 | empty |
| 2 | 168 | 0.54 | 0.80 | 36 | GDP, MG |
| 3 | 139 | 0.51 | 0.80 | 28 | GDP, MG |
| 4 | 108 | 0.44 | 0.78 | 20 | empty |
| 5 | 68 | 0.38 | 0.78 | 11 | 2XH |
Interfaces
1 interface between chains.
- A–B · 609 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4Q01 · 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 4Q01 · PDBe 4Q01 · UniProt P01116
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