Research workbench
Cryo-EM structure of dnmdp-induced PDE3A-SLFN12 complex
Analyse Cryo-EM structure of dnmdp-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
- 7EG1
- 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
- X5M, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 41% 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 | 57% helix, 2% strand | Q14432 |
| B, D | Schlafen family member 12 | protein | 567 | 31% helix, 17% strand | Q8IYM2 |
Ligands and binding sites
- X5M · (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one · ligand · 2 copies · chains A, B, C, D
- 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.83 | 0.93 | 38 | X5M, MG |
| 2 | 350 | 0.83 | 0.92 | 41 | X5M, MG |
| 3 | 1025 | 0.83 | 0.84 | 102 | empty |
| 4 | 834 | 0.81 | 0.84 | 61 | empty |
| 5 | 239 | 0.62 | 0.81 | 37 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3257 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1533 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1533 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 736 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 158 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7EG1 · Cryo-EM structure of DNMDP-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 7EG1 · PDBe 7EG1 · UniProt Q14432 · UniProt Q8IYM2
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