Research workbench
Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for CDC6 dephosphorylation
Analyse Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I5L
- Type
- protein
- Length
- 2,475 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, Q9Y5P8, Q99741, P67775
- Ligands
- 1ZN, FGA, MAA, CA, MN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 63% helix, 6% 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 | 79% helix, 0% strand | P30153 |
| B | SERINE/THREONINE-protein phosphatase 2A regulatory subunit B'' subunit beta - cell division control protein 6 homolog chimeric construct | protein | 356 | 62% helix, 6% strand | Q9Y5P8, Q99741 |
| C, F | SERINE/THREONINE-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha (EC 3.1.3.16) | protein | 295 | 37% helix, 18% strand | P67775 |
| E | SERINE/THREONINE-protein phosphatase 2A regulatory subunit B'' subunit beta - cell division control protein 6 homolog chimeric construct | protein | 357 | 62% helix, 5% strand | Q9Y5P8, Q99741 |
| G, H | Microcystin-lr (mclr) bound form | 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 F, G, C, H
- FGA · Gamma-D-glutamic acid · ligand · 2 copies · chains F, G, C, H
- MAA · N-methyl-L-alanine · ligand · 2 copies · chains F, G, C, H
- CA · Calcium ion · metal · 4 copies · chains B, E
- MN · Manganese (II) ion · metal · 4 copies · chains C, F
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, F, B, C, D, E
- MLI · Malonate ion · additive · 3 copies · chains C, E, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.81 | 0.82 | 95 | PEG |
| 2 | 897 | 0.75 | 0.78 | 83 | empty |
| 3 | 886 | 0.72 | 0.77 | 70 | empty |
| 4 | 236 | 0.57 | 0.79 | 34 | 1ZN, FGA, MAA, MN |
| 5 | 303 | 0.56 | 0.76 | 33 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1700 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1680 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1100 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1071 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 712 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 d-amino, 2 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 4I5L · Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6… · 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 0.99
- P30153 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A 65 kda… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9Y5P8
- Every structure of UniProt Q99741
- Every structure of UniProt P67775
- Elsewhere: RCSB PDB 4I5L · PDBe 4I5L · UniProt P30153 · UniProt Q9Y5P8 · UniProt Q99741 · UniProt P67775
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