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Crystal structure of PDE2 in complex with complex 9
Analyse Crystal structure of PDE2 in complex with complex 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B97
- Type
- protein
- Length
- 691 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.17
- UniProt
- O00408
- Ligands
- CZY, ZN, MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 343 | 67% helix, 0% strand | O00408 |
| B | Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 348 | 67% helix, 0% strand | O00408 |
Ligands and binding sites
- CZY · 6-chloro-1-methyl-N-{(1R)-1-[4-(trifluoromethyl) phenyl]ethyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.78 | 0.80 | 93 | EDO |
| 2 | 437 | 0.76 | 0.85 | 42 | MG, CZY |
| 3 | 427 | 0.76 | 0.85 | 41 | MG, CZY |
| 4 | 58 | 0.58 | 0.90 | 20 | empty |
| 5 | 61 | 0.28 | 0.73 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 833 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6B97 · Crystal structure of PDE2 in complex with complex 9 · the same entry in another collection · chain A against A, TM-score 1.00
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 O00408
- Elsewhere: RCSB PDB 6B97 · PDBe 6B97 · UniProt O00408
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