Research workbench
HRAS G12S in complex with GDP
Analyse HRAS G12S in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MQT
- Type
- protein
- Length
- 1,332 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS
- UniProt
- P01112
- Ligands
- GDP, MG
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | GTPase HRAS | protein | 167 | 39% helix, 25% strand | P01112 |
| B, C, G, H | GTPase HRAS | protein | 166 | 37% helix, 26% strand | P01112 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.61 | 0.76 | 43 | empty |
| 2 | 318 | 0.58 | 0.77 | 30 | empty |
| 3 | 277 | 0.57 | 0.78 | 38 | GDP, MG |
| 4 | 260 | 0.55 | 0.77 | 39 | empty |
| 5 | 276 | 0.53 | 0.75 | 29 | empty |
Interfaces
12 interfaces between chains.
- A–C · 538 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 533 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 329 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 317 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 261 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6MQT · HRAS G12S in complex with GDP · 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 6MQT · PDBe 6MQT · UniProt P01112
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