Research workbench
Crystal structure of protein phosphate 1 complexed with PP1 binding domain of gm
Analyse Crystal structure of protein phosphate 1 complexed with PP1 binding domain of gm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZQV
- Type
- protein
- Length
- 1,258 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit; Protein phosphatase 1…
- EC
- 3.1.3.16
- UniProt
- P62137, Q16821
- Ligands
- MN
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) | protein | 294 | 35% helix, 19% strand | P62137 |
| B | SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) | protein | 293 | 34% helix, 19% strand | P62137 |
| E, F, H | Protein phosphatase 1 regulatory subunit 3A | protein | 21 | 19% helix, 38% strand | Q16821 |
| G | Protein phosphatase 1 regulatory subunit 3A | protein | 20 | 0% helix, 40% strand | Q16821 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.72 | 0.81 | 56 | empty |
| 2 | 430 | 0.72 | 0.82 | 48 | empty |
| 3 | 182 | 0.51 | 0.78 | 23 | FLC |
| 4 | 169 | 0.51 | 0.78 | 22 | MN, FLC |
| 5 | 181 | 0.51 | 0.78 | 25 | FLC |
Interfaces
7 interfaces between chains.
- A–E · 1116 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 1100 Ų buried · 15 hydrogen bonds · protein-protein
- D–G · 1090 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1086 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 761 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5ZQV · Crystal Structure of Protein Phosphate 1 complexed with PP1 binding domain of GM · the same entry in another collection · chain H against H, TM-score 1.00
- P62137 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PP1-alpha… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q16821 · AlphaFold monomer V2.0 prediction for protein phosphatase 1 regulatory subunit 3A (Q16821) · a predicted model of the same protein · chain G against A, TM-score 0.22
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 P62137
- Every structure of UniProt Q16821
- Elsewhere: RCSB PDB 5ZQV · PDBe 5ZQV · UniProt P62137 · UniProt Q16821
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