MolNFT v1 · #181323 · protein
Cryo-EM of the SLFN12-PDE3A complex: consensus subset model
7LRD · Schlafen family member 12: “Cryo-EM of the SLFN12-PDE3A complex: consensus subset model”. Electron microscopy, 4 ligands (X5M, ZN, MN), 20 pockets (best druggability 0.84). MolNFT v1 #181323 on GenesisL1: 3D structure, binding sites…
- PDB
- 7LRD
- Type
- protein
- Length
- 1,766 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Schlafen family member 12; Cgmp-inhibited 3',5'-cyclic phosphodiesterase a
- EC
- 3.1.4.17
- UniProt
- Q8IYM2, Q14432
- Ligands
- X5M, ZN, MN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Schlafen family member 12 | protein | 512 | 36% helix, 26% strand | Q8IYM2 |
| B, D | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 371 | 63% helix, 3% strand | Q14432 |
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
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains B, D
- MG · Magnesium 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.84 | 0.95 | 34 | MG, X5M |
| 2 | 273 | 0.83 | 0.94 | 34 | MG, X5M |
| 3 | 618 | 0.71 | 0.79 | 59 | empty |
| 4 | 490 | 0.68 | 0.79 | 41 | empty |
| 5 | 583 | 0.68 | 0.77 | 79 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3047 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 881 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 557 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 556 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 102 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7LRD · Cryo-EM of the SLFN12-PDE3A complex: Consensus subset model · 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 B 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 A against A, TM-score 0.96
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 Q8IYM2
- Every structure of UniProt Q14432
- Elsewhere: RCSB PDB 7LRD · PDBe 7LRD · UniProt Q8IYM2 · UniProt Q14432
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