Research workbench
Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation T311A
Analyse Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WDE
- Type
- protein
- Length
- 427 residues
- Chains
- 2
- 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
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) | protein | 215 | 31% helix, 30% strand | P16330 |
| B | 2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) | protein | 212 | 30% helix, 31% strand | P16330 |
Ligands and binding sites
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.71 | 0.78 | 58 | empty |
| 2 | 467 | 0.64 | 0.77 | 47 | GOL |
| 3 | 327 | 0.57 | 0.76 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 352 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4WDE · Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation… · 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 B 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 P16330
- Elsewhere: RCSB PDB 4WDE · PDBe 4WDE · UniProt P16330
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.