Research workbench
Crystal structure of a protein phosphatase 2A (PP2A) holoenzyme.
Analyse Crystal structure of a protein phosphatase 2A (PP2A) holoenzyme. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IAE
- Type
- protein
- Length
- 2,524 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
- Q76MZ3, Q13362, P67775
- Ligands
- 1ZN, FGA, DAM, MN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 52% 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 (EC 3.1.3.16) | protein | 583 | 65% helix, 0% strand | Q76MZ3 |
| B | SERINE/THREONINE-protein phosphatase 2A 56 kda regulatory subunit gamma isoform (EC 3.1.3.16) | protein | 376 | 61% helix, 0% strand | Q13362 |
| C | SERINE/THREONINE-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) | protein | 306 | 30% helix, 18% strand | P67775 |
| E | SERINE/THREONINE-protein phosphatase 2A 56 kda regulatory subunit gamma isoform (EC 3.1.3.16) | protein | 377 | 58% helix, 0% strand | Q13362 |
| F | SERINE/THREONINE-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) | protein | 291 | 32% helix, 18% strand | P67775 |
| M, N | 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, M, F, N
- FGA · Gamma-D-glutamic acid · ligand · 2 copies · chains C, M, F, N
- DAM · N-methyl-alpha-beta-dehydroalanine · ligand · 2 copies · chains C, M, F, N
- 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.78 | 0.80 | 114 | 1ZN, FGA, DAM, MN |
| 2 | 470 | 0.77 | 0.85 | 66 | empty |
| 3 | 315 | 0.76 | 0.87 | 43 | empty |
| 4 | 287 | 0.69 | 0.84 | 29 | empty |
| 5 | 405 | 0.65 | 0.78 | 36 | empty |
Interfaces
13 interfaces between chains.
- A–C · 1360 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1290 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1029 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 993 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 957 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 3 modified, 2 d-amino (covalent ligand, nonstandard, D-amino acid).
Compared structures
- 2IAE · Crystal structure of a protein phosphatase 2A (PP2A) holoenzyme. · the same entry in another collection · chain N against N, 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 0.99
- 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 0.98
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 Q76MZ3
- Every structure of UniProt Q13362
- Every structure of UniProt P67775
- Elsewhere: RCSB PDB 2IAE · PDBe 2IAE · UniProt Q76MZ3 · UniProt Q13362 · UniProt P67775
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