MolNFT v1 · #180518 · protein
Crystal structure of the catalytic domain of human PDE3A bound to AMP
7L29 · Cgmp-inhibited 3',5'-cyclic phosphodiesterase a: “Crystal structure of the catalytic domain of human PDE3A bound to AMP”. X-ray diffraction, 4 ligands (AMP, MN, MG), 12 pockets (best druggability 0.79). MolNFT v1 #180518 on…
- PDB
- 7L29
- Type
- protein
- Length
- 1,473 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
- AMP, MN, MG, CA
- Pockets
- 12 · best druggability 0.79
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 | 366 | 61% helix, 2% strand | Q14432 |
| B | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 369 | 61% helix, 2% strand | Q14432 |
| C | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 368 | 61% helix, 2% strand | Q14432 |
| D | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 370 | 59% helix, 2% strand | Q14432 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains A
- ACT · Acetate ion · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.79 | 0.80 | 117 | ACT |
| 2 | 874 | 0.76 | 0.79 | 88 | AMP, MG |
| 3 | 733 | 0.74 | 0.80 | 75 | AMP, MG |
| 4 | 668 | 0.74 | 0.80 | 67 | AMP, MG |
| 5 | 480 | 0.72 | 0.81 | 45 | AMP, MG |
Interfaces
3 interfaces between chains.
- B–C · 1184 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 954 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 948 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7L29 · Crystal structure of the catalytic domain of human PDE3A bound to AMP · the same entry in another collection · chain D against D, 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 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 Q14432
- Elsewhere: RCSB PDB 7L29 · PDBe 7L29 · UniProt Q14432
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.