Research workbench
Cryo-EM structure of SHOC2-PP1C-mras holophosphatase complex
Analyse Cryo-EM structure of SHOC2-PP1C-mras holophosphatase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UPI
- Type
- protein
- Length
- 972 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein M-RAS; SERINE/THREONINE-protein phosphatase PP1-alpha catalytic…
- EC
- 3.6.5.2, 3.1.3.16
- UniProt
- O14807, P62136, Q9UQ13
- Ligands
- GTP, MN, MG, CL
- Pockets
- 9 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 28% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein M-RAS (EC 3.6.5.2) | protein | 174 | 33% helix, 25% strand | O14807 |
| B | SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) | protein | 293 | 35% helix, 19% strand | P62136 |
| C | Leucine-rich repeat protein shoc-2 | protein | 505 | 23% helix, 14% strand | Q9UQ13 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.86 | 0.90 | 95 | GTP, MG |
| 2 | 259 | 0.77 | 0.90 | 49 | empty |
| 3 | 140 | 0.67 | 0.88 | 31 | empty |
| 4 | 75 | 0.51 | 0.85 | 15 | empty |
| 5 | 168 | 0.47 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1564 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1018 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7UPI · Cryo-EM structure of SHOC2-PP1c-MRAS holophosphatase complex · the same entry in another collection · chain A against A, TM-score 1.00
- P62136 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PP1-alpha… · a predicted model of the same protein · chain B 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 A against A, TM-score 0.98
- Q9UQ13 · AlphaFold monomer V2.0 prediction for leucine-rich repeat protein shoc-2 (Q9UQ13) · a predicted model of the same protein · chain C 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 O14807
- Every structure of UniProt P62136
- Every structure of UniProt Q9UQ13
- Elsewhere: RCSB PDB 7UPI · PDBe 7UPI · UniProt O14807 · UniProt P62136 · UniProt Q9UQ13
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