MolNFT v1 · #47980 · protein
Crystal structure of the full-length simian virus 40 small T antigen complexed with the protein phosphatase 2A aalpha subunit
2PF4 · SERINE/THREONINE-protein phosphatase 2A 65 kda regulatory…: “Crystal structure of the full-length simian virus 40 small T antigen complexed with the protein phosphatase…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best…
- PDB
- 2PF4
- Type
- protein
- Length
- 2,904 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; Small…
- UniProt
- Q76MZ3, Q9W9P1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein phosphatase 2A 65 kda regulatory subunit a alpha isoform | protein | 575 | 69% helix, 0% strand | Q76MZ3 |
| B | SERINE/THREONINE-protein phosphatase 2A 65 kda regulatory subunit a alpha isoform | protein | 575 | 73% helix, 0% strand | Q76MZ3 |
| C, D | SERINE/THREONINE-protein phosphatase 2A 65 kda regulatory subunit a alpha isoform | protein | 577 | 71% helix, 0% strand | Q76MZ3 |
| E | Small T antigen | protein | 163 | 50% helix, 2% strand | Q9W9P1 |
| F | Small T antigen | protein | 152 | 50% helix, 0% strand | Q9W9P1 |
| G | Small T antigen | protein | 142 | 51% helix, 1% strand | Q9W9P1 |
| H | Small T antigen | protein | 143 | 45% helix, 1% strand | Q9W9P1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.82 | 0.84 | 96 | empty |
| 2 | 990 | 0.76 | 0.79 | 76 | empty |
| 3 | 579 | 0.75 | 0.82 | 52 | empty |
| 4 | 612 | 0.74 | 0.81 | 53 | empty |
| 5 | 1042 | 0.74 | 0.77 | 88 | empty |
Interfaces
19 interfaces between chains.
- B–D · 1561 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 993 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 961 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 937 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 932 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2PF4 · Crystal structure of the full-length simian virus 40 small t antigen complexed with the… · the same entry in another collection · chain H against H, TM-score 1.00
- Q76MZ3 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A 65 kda… · a predicted model of the same protein · chain C against A, TM-score 0.88
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 Q9W9P1
- Elsewhere: RCSB PDB 2PF4 · PDBe 2PF4 · UniProt Q76MZ3 · UniProt Q9W9P1
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