Research workbench
Crystal structure of MERS-cov NSP16/NSP10 complex bound to M7GPPPA
Analyse Crystal structure of MERS-cov NSP16/NSP10 complex bound to M7GPPPA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YNF
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NSP16 protein; NSP10 protein
- UniProt
- K0BWD0, K4LC41
- Ligands
- GTA, ZN
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NSP16 protein | protein | 293 | 31% helix, 22% strand | K0BWD0 |
| B | NSP10 protein | protein | 125 | 31% helix, 12% strand | K4LC41 |
Ligands and binding sites
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.53 | 0.76 | 48 | GTA |
| 2 | 123 | 0.48 | 0.79 | 20 | empty |
| 3 | 66 | 0.32 | 0.76 | 17 | empty |
| 4 | 54 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1003 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5YNF · Crystal structure of MERS-CoV nsp16/nsp10 complex bound to m7GpppA · 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 K0BWD0
- Every structure of UniProt K4LC41
- Elsewhere: RCSB PDB 5YNF · PDBe 5YNF · UniProt K0BWD0 · UniProt K4LC41
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