Research workbench
Crystal structure of the catalytic domain of unliganded PDE5
Analyse Crystal structure of the catalytic domain of unliganded PDE5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H40
- Type
- protein
- Length
- 311 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.35
- UniProt
- O76074
- Ligands
- ZN, MG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 311 | 66% helix, 0% strand | O76074 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.66 | 0.78 | 43 | MG |
| 2 | 70 | 0.58 | 0.89 | 22 | empty |
| 3 | 78 | 0.44 | 0.80 | 21 | empty |
| 4 | 72 | 0.37 | 0.77 | 15 | empty |
Compared structures
- 2H40 · Crystal structure of the catalytic domain of unliganded PDE5 · the same entry in another collection · chain A against A, TM-score 1.00
- O76074 · AlphaFold monomer V2.0 prediction for cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O76074
- Elsewhere: RCSB PDB 2H40 · PDBe 2H40 · UniProt O76074
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