Research workbench
The crystal structure of the phosphodiesterase 2A catalytic domain
Analyse The crystal structure of the phosphodiesterase 2A catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z1L
- Type
- protein
- Length
- 338 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.17
- UniProt
- O00408
- Ligands
- ZN, MG, PO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 338 | 67% helix, 0% strand | O00408 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.76 | 0.84 | 49 | MG, PO4 |
| 2 | 73 | 0.53 | 0.85 | 16 | empty |
| 3 | 104 | 0.39 | 0.76 | 16 | empty |
Compared structures
- 1Z1L · The Crystal Structure of the Phosphodiesterase 2A Catalytic Domain · the same entry in another collection · chain A against A, TM-score 1.00
- O00408 · AlphaFold monomer V2.0 prediction for cgmp-dependent 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O00408
- Elsewhere: RCSB PDB 1Z1L · PDBe 1Z1L · UniProt O00408
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