Research workbench
Crystal structure of the PP2A phosphatase activator YPA1 PTPA1 in complex with model substrate
Analyse Crystal structure of the PP2A phosphatase activator YPA1 PTPA1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IXP
- Type
- protein
- Length
- 1,268 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase 2A activator 1; Sin-ala-ala-pro-lys-nit
- Ligands
- NIT, SO4, CL
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | SERINE/THREONINE-protein phosphatase 2A activator 1 | protein | 310 | 60% helix, 1% strand | — |
| B, C | SERINE/THREONINE-protein phosphatase 2A activator 1 | protein | 316 | 58% helix, 2% strand | — |
| F, G, H, I | Sin-ala-ala-pro-lys-nit | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- NIT · 4-nitroaniline · ligand · 4 copies · chains C, F, A, G, D, H, B, I
- SO4 · Sulfate ion · ion · 4 copies · chains A, F, B, D
- CL · Chloride ion · ion · 2 copies · chains A, C, D
- SIN · Succinic acid · additive · 4 copies · chains A, C, F, G, B, D, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.83 | 0.87 | 107 | empty |
| 2 | 661 | 0.82 | 0.87 | 102 | empty |
| 3 | 63 | 0.70 | 0.96 | 21 | empty |
| 4 | 699 | 0.69 | 0.77 | 81 | CL |
| 5 | 264 | 0.60 | 0.79 | 28 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1194 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1187 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 408 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 207 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 covalent (additive adduct, covalent ligand).
Compared structures
- 2IXP · Crystal structure of the Pp2A phosphatase activator Ypa1 PTPA1 in complex with model… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2IXP · PDBe 2IXP
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