MolNFT v1 · #177361 · protein
Cryo-EM structure of nauclefine-induced PDE3A-SLFN12 complex
7EG4 · Cgmp-inhibited 3',5'-cyclic phosphodiesterase a: “Cryo-EM structure of nauclefine-induced PDE3A-SLFN12 complex”. Electron microscopy, 3 ligands (J36, MG, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #177361 on GenesisL1: 3D…
- PDB
- 7EG4
- Type
- protein
- Length
- 1,878 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-inhibited 3',5'-cyclic phosphodiesterase a; Schlafen family member 12
- EC
- 3.1.4.17
- UniProt
- Q14432, Q8IYM2
- Ligands
- J36, MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 372 | 59% helix, 2% strand | Q14432 |
| D, B | Schlafen family member 12 | protein | 567 | 30% helix, 17% strand | Q8IYM2 |
Ligands and binding sites
- J36 · Parvine · ligand · 2 copies · chains C, D, A, B
- MG · Magnesium ion · metal · 4 copies · chains C, A
- ZN · Zinc ion · metal · 2 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.84 | 0.94 | 39 | J36, MG |
| 2 | 313 | 0.84 | 0.94 | 39 | J36, MG |
| 3 | 709 | 0.81 | 0.85 | 57 | empty |
| 4 | 1103 | 0.80 | 0.82 | 88 | empty |
| 5 | 551 | 0.69 | 0.78 | 54 | empty |
Interfaces
6 interfaces between chains.
- D–B · 3467 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1558 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1555 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 756 Ų buried · 14 hydrogen bonds · protein-protein
- C–B · 213 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 7EG4 · Cryo-EM structure of nauclefine-induced PDE3A-SLFN12 complex · the same entry in another collection · chain C against C, 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 C against A, TM-score 0.99
- Q8IYM2 · AlphaFold monomer V2.0 prediction for schlafen family member 12 (Q8IYM2) · a predicted model of the same protein · chain D against A, TM-score 0.90
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
- Every structure of UniProt Q8IYM2
- Elsewhere: RCSB PDB 7EG4 · PDBe 7EG4 · UniProt Q14432 · UniProt Q8IYM2
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