Research workbench
Structure of a protein phosphatase 2A holoenzyme with B55 subunit
Analyse Structure of a protein phosphatase 2A holoenzyme with B55 subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DW8
- Type
- protein
- Length
- 2,590 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase 2A 65 kda regulatory subunit a alpha isoform…
- EC
- 3.1.3.16
- UniProt
- P30153, P63151, P67775
- Ligands
- 1ZN, FGA, DAM, MN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | SERINE/THREONINE-protein phosphatase 2A 65 kda regulatory subunit a alpha isoform | protein | 582 | 69% helix, 0% strand | P30153 |
| B, E | SERINE/THREONINE-protein phosphatase 2A 55 kda regulatory subunit B alpha isoform | protein | 421 | 7% helix, 43% strand | P63151 |
| C, F | SERINE/THREONINE-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) | protein | 288 | 36% helix, 19% 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.79 | 0.83 | 70 | empty |
| 2 | 881 | 0.79 | 0.82 | 77 | empty |
| 3 | 686 | 0.74 | 0.80 | 79 | empty |
| 4 | 112 | 0.72 | 0.92 | 26 | empty |
| 5 | 447 | 0.67 | 0.79 | 50 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1969 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1951 Ų buried · 37 hydrogen bonds · protein-protein
- D–F · 1050 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1017 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 373 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 d-amino, 2 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 3DW8 · Structure of a Protein Phosphatase 2A Holoenzyme with B55 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 C against A, TM-score 1.00
- P63151 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A 55 kda… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P30153
- Every structure of UniProt P63151
- Every structure of UniProt P67775
- Elsewhere: RCSB PDB 3DW8 · PDBe 3DW8 · UniProt P30153 · UniProt P63151 · UniProt P67775
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