Research workbench
Cryo-EM structure of anagrelide-induced PDE3A-SLFN12 complex
Analyse Cryo-EM structure of anagrelide-induced PDE3A-SLFN12 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EG0
- 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
- J33, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 372 | 59% helix, 2% strand | Q14432 |
| B, D | Schlafen family member 12 | protein | 567 | 31% helix, 17% strand | Q8IYM2 |
Ligands and binding sites
- J33 · 6,7-bis(chloranyl)-3,5-dihydro-1H-imidazo[2,1-b]quinazolin-2-one · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.83 | 0.94 | 38 | J33, MG |
| 2 | 292 | 0.83 | 0.94 | 36 | J33, MG |
| 3 | 944 | 0.82 | 0.83 | 69 | empty |
| 4 | 1174 | 0.81 | 0.82 | 96 | empty |
| 5 | 585 | 0.70 | 0.79 | 73 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3316 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1506 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1502 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 785 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 173 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7EG0 · Cryo-EM structure of anagrelide-induced PDE3A-SLFN12 complex · the same entry in another collection · chain A against A, 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
- Q8IYM2 · AlphaFold monomer V2.0 prediction for schlafen family member 12 (Q8IYM2) · a predicted model of the same protein · chain B 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 7EG0 · PDBe 7EG0 · UniProt Q14432 · UniProt Q8IYM2
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