MolNFT v1 · #54915 · protein
Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, complexed with sulfate
2Y3X · 2', 3'-cyclic-nucleotide 3'-phosphodiesterase: “Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, complexed with sulfate”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 2Y3X
- Type
- protein
- Length
- 640 residues
- Chains
- 3
- 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
- SO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2', 3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) | protein | 215 | 34% helix, 31% strand | P16330 |
| B | 2', 3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) | protein | 215 | 32% helix, 31% strand | P16330 |
| E | 2', 3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) | protein | 210 | 33% helix, 31% strand | P16330 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.73 | 0.80 | 48 | empty |
| 2 | 379 | 0.67 | 0.80 | 47 | empty |
| 3 | 335 | 0.64 | 0.79 | 37 | GOL, SO4 |
| 4 | 285 | 0.63 | 0.80 | 32 | SO4 |
| 5 | 290 | 0.55 | 0.76 | 31 | SO4 |
Interfaces
3 interfaces between chains.
- B–E · 363 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 311 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 303 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2Y3X · Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, complexed with… · 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 E against A, TM-score 0.96
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 2Y3X · PDBe 2Y3X · UniProt P16330
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.