Research workbench
Crystal structure of protein phosphatase 2A (PP2A) holoenzyme with the catalytic subunit carboxyl terminus truncated
Analyse Crystal structure of protein phosphatase 2A (PP2A) holoenzyme with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NYL
- Type
- protein
- Length
- 2,534 residues
- Chains
- 8
- 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, Q13362, P67775
- Ligands
- 1ZN, FGA, DAM, MN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein phosphatase 2, regulatory subunit a (pr 65), alpha isoform | protein | 582 | 72% helix, 0% strand | Q96DH3 |
| B, E | SERINE/THREONINE-protein phosphatase 2A 56 kda regulatory subunit gamma isoform | protein | 388 | 59% helix, 0% strand | Q13362 |
| C, F | SERINE/THREONINE-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) | protein | 293 | 36% helix, 17% strand | P67775 |
| G, H | 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 · 2 copies · chains C, G, F, H
- FGA · Gamma-D-glutamic acid · ligand · 2 copies · chains C, G, F, H
- DAM · N-methyl-alpha-beta-dehydroalanine · ligand · 2 copies · chains C, G, F, H
- MN · Manganese (II) ion · metal · 4 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.81 | 0.82 | 80 | empty |
| 2 | 976 | 0.81 | 0.82 | 85 | empty |
| 3 | 344 | 0.63 | 0.79 | 46 | 1ZN, FGA, DAM |
| 4 | 338 | 0.63 | 0.79 | 42 | 1ZN, FGA, DAM, MN |
| 5 | 284 | 0.58 | 0.78 | 41 | empty |
Interfaces
10 interfaces between chains.
- A–C · 1093 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1049 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 965 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 960 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 727 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 modified, 6 covalent, 2 d-amino (engineered, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 2NYL · Crystal structure of Protein Phosphatase 2A (PP2A) holoenzyme with the catalytic subunit… · the same entry in another collection · chain H against H, 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 F against A, TM-score 1.00
- Q13362 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A 56 kda… · a predicted model of the same protein · chain E against A, TM-score 0.97
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 Q13362
- Every structure of UniProt P67775
- Elsewhere: RCSB PDB 2NYL · PDBe 2NYL · UniProt Q96DH3 · UniProt Q13362 · UniProt P67775
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