Research workbench
Crystal structure of the catalytic domain of human PDE3A bound to dnmdp
Analyse Crystal structure of the catalytic domain of human PDE3A bound to dnmdp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KWE
- Type
- protein
- Length
- 1,464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-inhibited 3',5'-cyclic phosphodiesterase a
- EC
- 3.1.4.17
- UniProt
- Q14432
- Ligands
- X5M, MN, MG
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 363 | 60% helix, 2% strand | Q14432 |
| D | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 371 | 59% helix, 2% strand | Q14432 |
| C | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 365 | 61% helix, 2% strand | Q14432 |
| B | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 365 | 59% helix, 2% strand | Q14432 |
Ligands and binding sites
- X5M · (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one · ligand · 4 copies · chains A, D, C, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, D, C, B
- MG · Magnesium ion · metal · 4 copies · chains A, D, C, B
- ACT · Acetate ion · additive · 4 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.76 | 0.78 | 114 | ACT |
| 2 | 900 | 0.75 | 0.79 | 109 | X5M, MG |
| 3 | 747 | 0.75 | 0.79 | 81 | X5M, MG |
| 4 | 587 | 0.73 | 0.81 | 61 | X5M, MG |
| 5 | 468 | 0.71 | 0.81 | 50 | X5M, MG |
Interfaces
3 interfaces between chains.
- C–B · 1154 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 955 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 924 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7KWE · Crystal structure of the catalytic domain of human PDE3A bound to DNMDP · the same entry in another collection · chain B against B, TM-score 1.00
- Q14432 · AlphaFold monomer V2.0 prediction for cgmp-inhibited 3',5'-cyclic phosphodiesterase a… · a predicted model of the same protein · chain A 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 Q14432
- Elsewhere: RCSB PDB 7KWE · PDBe 7KWE · UniProt Q14432
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