Research workbench
Allosteric modulation of H-RAS GTPase
Analyse Allosteric modulation of H-RAS GTPase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K9L
- Type
- protein
- Length
- 475 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS
- UniProt
- P01112
- Ligands
- GNP, MG, CA
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS | protein | 159 | 33% helix, 28% strand | P01112 |
| B | GTPase HRAS | protein | 158 | 36% helix, 28% strand | P01112 |
| C | GTPase HRAS | protein | 158 | 36% helix, 25% strand | P01112 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CA · Calcium 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.78 | 0.83 | 64 | empty |
| 2 | 149 | 0.48 | 0.78 | 27 | MG, GNP |
| 3 | 110 | 0.41 | 0.77 | 25 | empty |
| 4 | 117 | 0.40 | 0.75 | 26 | MG, GNP |
| 5 | 92 | 0.35 | 0.75 | 23 | MG, GNP |
Interfaces
3 interfaces between chains.
- A–B · 917 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 346 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 326 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3K9L · Allosteric modulation of H-Ras GTPase · 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 3K9L · PDBe 3K9L · UniProt P01112
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