MolNFT v1 · #147006 · protein
HRAS G13D bound to GDP (H13GDP)
6DZH · GTPase HRAS: “HRAS G13D bound to GDP (H13GDP)”. X-ray diffraction, 3 ligands (GDP, MG, CA), 4 pockets (best druggability 0.60). MolNFT v1 #147006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DZH
- Type
- protein
- Length
- 472 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS
- UniProt
- P01112
- Ligands
- GDP, MG, CA
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS | protein | 165 | 36% helix, 25% strand | P01112 |
| B | GTPase HRAS | protein | 154 | 33% helix, 25% strand | P01112 |
| C | GTPase HRAS | protein | 153 | 37% helix, 26% strand | P01112 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
- CA · Calcium ion · metal · 2 copies · chains A, B, C
- GOL · Glycerol · additive · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.60 | 0.82 | 31 | GDP, MG, CA |
| 2 | 163 | 0.45 | 0.76 | 32 | GDP, MG |
| 3 | 140 | 0.44 | 0.76 | 26 | empty |
| 4 | 119 | 0.39 | 0.75 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–C · 941 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 502 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6DZH · HRAS G13D bound to GDP (H13GDP) · 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 6DZH · PDBe 6DZH · UniProt P01112
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.