Research workbench
Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with sildenafil
Analyse Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JWQ
- Type
- protein
- Length
- 1,298 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific 3',5'-cyclic phosphodiesterase catalytic domain, cone cgmp-specific…
- EC
- 3.1.4.35
- UniProt
- O76074, P51160
- Ligands
- VIA, ZN, MG
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cgmp-specific 3',5'-cyclic phosphodiesterase catalytic domain, cone cgmp-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera (EC 3.1.4.35) | protein | 324 | 69% helix, 0% strand | O76074, P51160 |
| C | Cgmp-specific 3',5'-cyclic phosphodiesterase catalytic domain, cone cgmp-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera (EC 3.1.4.35) | protein | 327 | 69% helix, 0% strand | O76074, P51160 |
| D | Cgmp-specific 3',5'-cyclic phosphodiesterase catalytic domain, cone cgmp-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera (EC 3.1.4.35) | protein | 323 | 69% helix, 0% strand | O76074, P51160 |
Ligands and binding sites
- VIA · 5-{2-ethoxy-5-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}-1-methyl-3-propyl-1H,6H,7H-pyrazolo[4,3-d]pyrimidin-7-one · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.85 | 0.86 | 94 | MG, VIA |
| 2 | 608 | 0.83 | 0.88 | 64 | MG, VIA |
| 3 | 1070 | 0.81 | 0.82 | 103 | MG, VIA |
| 4 | 1078 | 0.79 | 0.80 | 105 | MG, VIA |
| 5 | 614 | 0.72 | 0.79 | 56 | empty |
Interfaces
5 interfaces between chains.
- C–D · 584 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 568 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 566 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 486 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3JWQ · Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with sildenafil · 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 D against A, TM-score 0.99
- P51160 · AlphaFold monomer V2.0 prediction for cone cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain D 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 O76074
- Every structure of UniProt P51160
- Elsewhere: RCSB PDB 3JWQ · PDBe 3JWQ · UniProt O76074 · UniProt P51160
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