Research workbench
X-ray crystal structure of dihydromicrocystin-la bound to protein phosphatase-1
Analyse X-ray crystal structure of dihydromicrocystin-la bound to protein phosphatase-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BDX
- Type
- protein
- Length
- 297 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE protein phosphatase PP1-gamma catalytic subunit; Dihydromicrocystin-la
- EC
- 3.1.3.16
- UniProt
- P36873
- Ligands
- 1ZN, FGA, MAA, MN
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE protein phosphatase PP1-gamma catalytic subunit (EC 3.1.3.16) | protein | 293 | 34% helix, 19% strand | P36873 |
| B | Dihydromicrocystin-la | 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 · chains A, B
- FGA · Gamma-D-glutamic acid · ligand · chains A, B
- MAA · N-methyl-L-alanine · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.55 | 0.79 | 28 | FGA, MAA, MN |
| 2 | 52 | 0.32 | 0.77 | 11 | empty |
| 3 | 72 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 218 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 d-amino, 1 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 2BDX · X-ray Crystal Structure of dihydromicrocystin-LA bound to Protein Phosphatase-1 · the same entry in another collection · chain A against A, TM-score 1.00
- P36873 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PP1-gamma… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P36873
- Elsewhere: RCSB PDB 2BDX · PDBe 2BDX · UniProt P36873
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