MolNFT v1 · #102377 · protein
Crystal structure of yeast phosphodiesterase-1 in complex with gmp
4OJX · 3',5'-cyclic-nucleotide phosphodiesterase 1: “Crystal structure of yeast phosphodiesterase-1 in complex with gmp”. X-ray diffraction, 2 ligands (5GP, ZN), 3 pockets (best druggability 0.62). MolNFT v1 #102377 on GenesisL1: 3D…
- PDB
- 4OJX
- Type
- protein
- Length
- 363 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3',5'-cyclic-nucleotide phosphodiesterase 1
- EC
- 3.1.4.17
- UniProt
- P22434
- Ligands
- 5GP, ZN
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3',5'-cyclic-nucleotide phosphodiesterase 1 (EC 3.1.4.17) | protein | 363 | 31% helix, 26% strand | P22434 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.62 | 0.80 | 34 | MPD |
| 2 | 68 | 0.34 | 0.76 | 17 | empty |
| 3 | 60 | 0.31 | 0.75 | 11 | empty |
Compared structures
- 4OJX · crystal structure of yeast phosphodiesterase-1 in complex with GMP · the same entry in another collection · chain A against A, TM-score 1.00
- P22434 · AlphaFold monomer V2.0 prediction for 3',5'-cyclic-nucleotide phosphodiesterase 1 (P22434) · 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 P22434
- Elsewhere: RCSB PDB 4OJX · PDBe 4OJX · UniProt P22434
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