Research workbench
Human phosphodiestrase-5'GMP complex (ep), produced by soaking with 20MM CGMP+20 mm MNCL2+20 mm MGCL2 for 2 hours, and flash-cooled to liquid nitrogen temperature when substrate was still abudant.
Analyse Human phosphodiestrase-5'GMP complex (ep), produced by soaking with 20MM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DYS
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A
- EC
- 3.1.4.35
- UniProt
- O76083
- Ligands
- 5GP, IBM, MN, MG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 324 | 71% helix, 0% strand | O76083 |
| B | High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 328 | 72% helix, 0% strand | O76083 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · chains A
- IBM · 3-isobutyl-1-methylxanthine · ligand · chains B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.74 | 0.85 | 41 | MG, 5GP |
| 2 | 346 | 0.73 | 0.84 | 40 | MG, IBM, FMT |
| 3 | 88 | 0.44 | 0.80 | 24 | empty |
| 4 | 70 | 0.42 | 0.80 | 15 | empty |
| 5 | 84 | 0.36 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3DYS · human phosphodiestrase-5'GMP complex (EP), produced by soaking with 20mM cGMP+20 mM… · the same entry in another collection · chain A against A, TM-score 1.00
- O76083 · AlphaFold monomer V2.0 prediction for high affinity cgmp-specific 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O76083
- Elsewhere: RCSB PDB 3DYS · PDBe 3DYS · UniProt O76083
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