Research workbench
Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, crystallized with 2'-amps
Analyse Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YOZ
- Type
- protein
- Length
- 211 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-cyclic nucleotide 3'-phosphodiesterase
- EC
- 3.1.4.37
- UniProt
- P16330
- Ligands
- OVE, CL
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-cyclic nucleotide 3'-phosphodiesterase (EC 3.1.4.37) | protein | 211 | 32% helix, 32% strand | P16330 |
Ligands and binding sites
- OVE · 2'-O-(sulfidophosphinato)adenosine · ligand · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 4 copies · chains A
- GOL · Glycerol · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.61 | 0.78 | 34 | OVE, ACT |
| 2 | 50 | 0.35 | 0.78 | 12 | ACT |
Compared structures
- 2YOZ · Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, crystallized… · the same entry in another collection · chain A against A, TM-score 1.00
- P16330 · AlphaFold monomer V2.0 prediction for 2',3'-cyclic-nucleotide 3'-phosphodiesterase… · a predicted model of the same protein · chain A 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 P16330
- Elsewhere: RCSB PDB 2YOZ · PDBe 2YOZ · UniProt P16330
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