Research workbench
Structure of the protein phosphatase 2A core enzyme bound to tumor- inducing toxins
Analyse Structure of the protein phosphatase 2A core enzyme bound to tumor- inducing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IE3
- Type
- protein
- Length
- 873 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein phosphatase 2, regulatory subunit a (pr 65), alpha isoform…
- EC
- 3.1.3.16
- UniProt
- Q96DH3, P67775
- Ligands
- 1ZN, FGA, DAM, MN
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein phosphatase 2, regulatory subunit a (pr 65), alpha isoform | protein | 581 | 78% helix, 0% strand | Q96DH3 |
| C | SERINE/THREONINE-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) | protein | 288 | 35% helix, 18% strand | P67775 |
| I | Microcystin lr | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 1ZN · (2S,3S,4E,6E,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid · ligand · chains C, I
- FGA · Gamma-D-glutamic acid · ligand · chains C, I
- DAM · N-methyl-alpha-beta-dehydroalanine · ligand · chains C, I
- MN · Manganese (II) ion · metal · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.55 | 0.79 | 28 | FGA, DAM, MN |
| 2 | 149 | 0.52 | 0.80 | 27 | empty |
| 3 | 223 | 0.48 | 0.74 | 33 | empty |
| 4 | 85 | 0.32 | 0.73 | 18 | empty |
| 5 | 66 | 0.31 | 0.75 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–C · 987 Ų buried · 21 hydrogen bonds · protein-protein
- C–I · 241 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 d-amino, 1 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 2IE3 · Structure of the Protein Phosphatase 2A Core Enzyme Bound to Tumor-inducing Toxins · the same entry in another collection · chain A against A, TM-score 1.00
- P67775 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A catalytic… · a predicted model of the same protein · chain C 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 Q96DH3
- Every structure of UniProt P67775
- Elsewhere: RCSB PDB 2IE3 · PDBe 2IE3 · UniProt Q96DH3 · UniProt P67775
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