Research workbench
PP1 Y134K in complex with microcystin lr
Analyse PP1 Y134K in complex with microcystin lr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OBU
- Type
- protein
- Length
- 594 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit; Microcystin lr
- EC
- 3.1.3.16
- UniProt
- P62136
- Ligands
- 1ZN, FGA, DAM, MN, CL
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 33% 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 | 33% helix, 19% strand | P62136 |
| C, D | Microcystin lr | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 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
- DAM · N-methyl-alpha-beta-dehydroalanine · ligand · 2 copies · chains A, C, B, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 7 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.58 | 0.78 | 39 | 1ZN, FGA, DAM |
| 2 | 213 | 0.55 | 0.78 | 31 | 1ZN, FGA, MN |
| 3 | 123 | 0.50 | 0.81 | 33 | empty |
| 4 | 150 | 0.47 | 0.77 | 23 | GOL |
| 5 | 101 | 0.45 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 748 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 236 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 235 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 d-amino, 2 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
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 6OBU · PDBe 6OBU · UniProt P62136
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