Research workbench
Crystal structure of PDE5A gaf domain (89-518)
Analyse Crystal structure of PDE5A gaf domain (89-518) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MF0
- Type
- protein
- Length
- 747 residues
- Chains
- 2
- 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
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 378 | 39% helix, 19% strand | O76074 |
| B | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) | protein | 369 | 37% helix, 20% strand | O76074 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.69 | 0.82 | 24 | empty |
| 2 | 470 | 0.64 | 0.77 | 49 | empty |
| 3 | 423 | 0.61 | 0.76 | 50 | empty |
| 4 | 236 | 0.58 | 0.79 | 22 | empty |
| 5 | 152 | 0.55 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2758 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
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 3MF0 · PDBe 3MF0 · UniProt O76074
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