Research workbench
Cryo-EM structure of the SHOC2:PP1C:MRAS complex
Analyse Cryo-EM structure of the SHOC2:PP1C:MRAS complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SD0
- Type
- protein
- Length
- 965 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat protein shoc-2; RAS-related protein M-RAS; SERINE/THREONINE-protein…
- EC
- 3.6.5.2, 3.1.3.16
- UniProt
- Q9UQ13, O14807, P36873
- Ligands
- GCP, MN, MG
- Pockets
- 9 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 28% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat protein shoc-2 | protein | 499 | 20% helix, 12% strand | Q9UQ13 |
| B | RAS-related protein M-RAS (EC 3.6.5.2) | protein | 174 | 37% helix, 22% strand | O14807 |
| C | SERINE/THREONINE-protein phosphatase PP1-gamma catalytic subunit (EC 3.1.3.16) | protein | 292 | 35% helix, 17% strand | P36873 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains B
- MN · Manganese (II) ion · metal · 2 copies · chains C
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.85 | 0.87 | 83 | GCP, MG |
| 2 | 283 | 0.81 | 0.92 | 48 | empty |
| 3 | 855 | 0.80 | 0.83 | 81 | empty |
| 4 | 50 | 0.70 | 0.97 | 16 | empty |
| 5 | 183 | 0.61 | 0.83 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1225 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1041 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 627 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7SD0 · Cryo-EM structure of the SHOC2:PP1C:MRAS complex · the same entry in another collection · chain A against A, TM-score 1.00
- P36873 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PP1-gamma… · a predicted model of the same protein · chain C against A, TM-score 0.99
- O14807 · AlphaFold monomer V2.0 prediction for RAS-related protein M-RAS (O14807) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q9UQ13 · AlphaFold monomer V2.0 prediction for leucine-rich repeat protein shoc-2 (Q9UQ13) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9UQ13
- Every structure of UniProt O14807
- Every structure of UniProt P36873
- Elsewhere: RCSB PDB 7SD0 · PDBe 7SD0 · UniProt Q9UQ13 · UniProt O14807 · UniProt P36873
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