MolNFT v1 · #147234 · protein
HRAS G13D bound to gppnhp (HA,B,C13GNP)
6E6P · GTPase HRAS: “HRAS G13D bound to gppnhp (HA,B,C13GNP)”. X-ray diffraction, 4 ligands (GNP, MG, CA), 5 pockets (best druggability 0.58). MolNFT v1 #147234 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6E6P
- Type
- protein
- Length
- 483 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS
- EC
- 3.6.5.2
- UniProt
- P01112
- Ligands
- GNP, MG, CA, NA
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS (EC 3.6.5.2) | protein | 159 | 36% helix, 26% strand | P01112 |
| B | GTPase HRAS (EC 3.6.5.2) | protein | 158 | 35% helix, 26% strand | P01112 |
| C | GTPase HRAS (EC 3.6.5.2) | protein | 166 | 38% helix, 27% 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, C
- NA · Sodium ion · metal · chains C
- GOL · Glycerol · additive · 4 copies · chains A, C, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.58 | 0.78 | 35 | GNP, MG |
| 2 | 189 | 0.55 | 0.79 | 35 | GOL |
| 3 | 144 | 0.50 | 0.79 | 27 | GNP, MG |
| 4 | 109 | 0.40 | 0.76 | 28 | empty |
| 5 | 105 | 0.37 | 0.74 | 21 | GNP, MG |
Interfaces
2 interfaces between chains.
- A–C · 824 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 517 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6E6P · HRAS G13D bound to GppNHp (Ha,b,c13GNP) · 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 6E6P · PDBe 6E6P · UniProt P01112
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