MolNFT v1 · #22594 · protein
Catalytic domain of human phosphodiesterase 5A in complex with gmp
1T9S · Cgmp-specific 3',5'-cyclic phosphodiesterase: “Catalytic domain of human phosphodiesterase 5A in complex with gmp”. X-ray diffraction, 3 ligands (5GP, ZN, MG), 7 pockets (best druggability 0.75). MolNFT v1 #22594 on GenesisL1: 3D…
- PDB
- 1T9S
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-specific 3',5'-cyclic phosphodiesterase
- EC
- 3.1.4.17
- UniProt
- O76074
- Ligands
- 5GP, ZN, MG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) | protein | 326 | 72% helix, 0% strand | O76074 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.75 | 0.78 | 77 | empty |
| 2 | 493 | 0.73 | 0.82 | 44 | MG, 5GP |
| 3 | 480 | 0.72 | 0.82 | 46 | MG, 5GP |
| 4 | 67 | 0.53 | 0.87 | 20 | empty |
| 5 | 74 | 0.53 | 0.86 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1T9S · Catalytic Domain Of Human Phosphodiesterase 5A in Complex with GMP · 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 A against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 1T9S · PDBe 1T9S · UniProt O76074
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