Research workbench
Crystal structure of a complex between protein phosphatase 1 alpha (PP1), the PP1 binding and PDZ domains of spinophilin and the small natural molecular toxin nodularin-R
Analyse Crystal structure of a complex between protein phosphatase 1 alpha (PP1), the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EGH
- Type
- protein
- Length
- 816 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit; Spinophilin; Nodularin R
- EC
- 3.1.3.16
- UniProt
- P62136, O35274
- Ligands
- ACB, 1ZN, FGA, MDH, MN
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 24% 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 | 294 | 35% helix, 20% strand | P62136 |
| C | Spinophilin | protein | 160 | 18% helix, 33% strand | O35274 |
| D | Spinophilin | protein | 66 | 17% helix, 18% strand | O35274 |
| E, F | Nodularin R | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACB · 3-methyl-beta-D-aspartic acid · ligand · 2 copies · chains A, E, B, F
- 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, E, B, F
- FGA · Gamma-D-glutamic acid · ligand · 2 copies · chains A, E, B, F
- MDH · N-methyldehydrobutyrine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.68 | 0.76 | 66 | empty |
| 2 | 253 | 0.58 | 0.78 | 27 | empty |
| 3 | 159 | 0.46 | 0.76 | 27 | 1ZN, FGA, MN |
| 4 | 91 | 0.43 | 0.79 | 20 | empty |
| 5 | 135 | 0.41 | 0.75 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2087 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 2083 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 403 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3EGH · Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1), the PP1 binding… · the same entry in another collection · chain D against D, 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
- O35274 · AlphaFold monomer V2.0 prediction for neurabin-2 (O35274) · a predicted model of the same protein · chain D against A, TM-score 0.94
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
- Every structure of UniProt O35274
- Elsewhere: RCSB PDB 3EGH · PDBe 3EGH · UniProt P62136 · UniProt O35274
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