MolNFT v1 · #62154 · protein
Crystal structure of protein phosphatase-1 bound to the natural toxin nodularin-R
3E7A · SERINE/THREONINE-protein phosphatase PP1-alpha catalytic…: “Crystal structure of protein phosphatase-1 bound to the natural toxin nodularin-R”. X-ray diffraction, 8 ligands (ACB, 1ZN, FGA), 8 pockets (best druggability 0.54). MolNFT…
- PDB
- 3E7A
- Type
- protein
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit; Nodularin R
- EC
- 3.1.3.16
- UniProt
- P62136
- Ligands
- ACB, 1ZN, FGA, MDH, MN, IOD, CL, AZI
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) | protein | 293 | 35% helix, 19% strand | P62136 |
| C, D | Nodularin R | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACB · 3-methyl-beta-D-aspartic acid · ligand · 2 copies · chains A, C, B, D
- 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 A, C, B, D
- FGA · Gamma-D-glutamic acid · ligand · 2 copies · chains A, C, B, D
- MDH · N-methyldehydrobutyrine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- IOD · Iodide ion · ion · 14 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- AZI · Azide ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.54 | 0.80 | 31 | empty |
| 2 | 146 | 0.48 | 0.78 | 20 | IOD |
| 3 | 168 | 0.48 | 0.76 | 24 | IOD |
| 4 | 79 | 0.43 | 0.80 | 16 | empty |
| 5 | 112 | 0.42 | 0.76 | 21 | 1ZN, FGA, MN |
Interfaces
3 interfaces between chains.
- A–B · 651 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 100 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 79 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3E7A · Crystal Structure of Protein Phosphatase-1 Bound to the natural toxin Nodularin-R · the same entry in another collection · chain C against C, TM-score 1.00
- P62136 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PP1-alpha… · a predicted model of the same protein · chain B 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
- Every structure of UniProt P62136
- Elsewhere: RCSB PDB 3E7A · PDBe 3E7A · UniProt P62136
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