MolNFT v1 · #177889 · protein
Crystal structure of ebinur lake virus cap snatching endonuclease in complex with inhibitor 16
7EX7 · Replicase: “Crystal structure of ebinur lake virus cap snatching endonuclease in complex with inhibitor 16”. X-ray diffraction, 3 ligands (1I6, MN, CL), 6 pockets (best druggability 0.58). MolNFT v1 #177889 on GenesisL1: 3D…
- PDB
- 7EX7
- Type
- protein
- Length
- 701 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase
- EC
- 2.7.7.48
- UniProt
- A0A059WLS9
- Ligands
- 1I6, MN, CL
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Replicase (EC 2.7.7.48) | protein | 172 | 52% helix, 14% strand | A0A059WLS9 |
| C | Replicase (EC 2.7.7.48) | protein | 177 | 50% helix, 14% strand | A0A059WLS9 |
| D | Replicase (EC 2.7.7.48) | protein | 180 | 53% helix, 13% strand | A0A059WLS9 |
Ligands and binding sites
- 1I6 · Methyl (Z)-4-(4-(4-chlorobenzyl)-1-(3-methoxybenzyl) piperidin-4-yl)-2-hydroxy-4-oxobut-2-enoate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.58 | 0.75 | 41 | empty |
| 2 | 132 | 0.54 | 0.81 | 26 | empty |
| 3 | 172 | 0.44 | 0.74 | 23 | empty |
| 4 | 60 | 0.32 | 0.76 | 12 | empty |
| 5 | 54 | 0.29 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 530 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 327 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 270 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 85 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 56 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7EX7 · Crystal structure of Ebinur Lake virus cap snatching endonuclease in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A059WLS9
- Elsewhere: RCSB PDB 7EX7 · PDBe 7EX7 · UniProt A0A059WLS9
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