Research workbench
Crystal structure of protein phosphatase 2A (PP2A) with C-terminus truncated catalytic subunit
Analyse Crystal structure of protein phosphatase 2A (PP2A) with C-terminus truncated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NYM
- Type
- protein
- Length
- 2,534 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein phosphatase 2; SERINE/THREONINE-protein phosphatase 2A 56 kda regulatory subunit…
- EC
- 3.1.3.16
- UniProt
- Q96DH3, Q13362, P67775
- Ligands
- 1ZN, FGA, DAM, MN
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein phosphatase 2 | protein | 582 | 71% helix, 0% strand | Q96DH3 |
| B, E | SERINE/THREONINE-protein phosphatase 2A 56 kda regulatory subunit gamma isoform | protein | 388 | 61% helix, 0% strand | Q13362 |
| C, F | SERINE/THREONINE-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) | protein | 293 | 36% helix, 21% 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.74 | 0.80 | 59 | empty |
| 2 | 652 | 0.72 | 0.79 | 55 | empty |
| 3 | 495 | 0.71 | 0.81 | 55 | empty |
| 4 | 308 | 0.71 | 0.84 | 34 | empty |
| 5 | 338 | 0.63 | 0.79 | 41 | 1ZN, FGA, DAM |
Interfaces
10 interfaces between chains.
- A–C · 1111 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 1100 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 995 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 994 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 779 Ų buried · 10 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
- 2NYM · Crystal Structure of Protein Phosphatase 2A (PP2A) with C-terminus truncated catalytic… · 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 2NYM · PDBe 2NYM · UniProt Q96DH3 · UniProt Q13362 · UniProt P67775
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