MolNFT v1 · #140822 · protein
Crystal structure of MERS-cov NSP16/NSP10 complex bound to M7GPPPG
5YNJ · NSP16 protein: “Crystal structure of MERS-cov NSP16/NSP10 complex bound to M7GPPPG”. X-ray diffraction, 2 ligands (GTG, ZN), 4 pockets (best druggability 0.48). MolNFT v1 #140822 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5YNJ
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NSP16 protein; NSP10 protein
- UniProt
- K0BWD0, K4LC41
- Ligands
- GTG, ZN
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NSP16 protein | protein | 293 | 30% helix, 22% strand | K0BWD0 |
| B | NSP10 protein | protein | 124 | 30% helix, 14% strand | K4LC41 |
Ligands and binding sites
- GTG · 7-methyl-guanosine-5'-triphosphate-5'-guanosine · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.48 | 0.74 | 35 | GTG |
| 2 | 138 | 0.47 | 0.77 | 26 | empty |
| 3 | 53 | 0.28 | 0.75 | 15 | empty |
| 4 | 50 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 987 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5YNJ · Crystal structure of MERS-CoV nsp16/nsp10 complex bound to m7GpppG · 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 5YNJ · PDBe 5YNJ · UniProt K0BWD0 · UniProt K4LC41
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