MolNFT v1 · #140824 · protein
Crystal structure of MERS-cov NSP16/NSP10 complex bound to SAM and M7GPPPA
5YNM · NSP16 protein: “Crystal structure of MERS-cov NSP16/NSP10 complex bound to SAM and M7GPPPA”. X-ray diffraction, 3 ligands (SAM, GTA, ZN), 2 pockets (best druggability 0.52). MolNFT v1 #140824 on GenesisL1: 3D structure, binding…
- PDB
- 5YNM
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NSP16 protein; NSP10 protein
- UniProt
- K0BWD0, K4LC41
- Ligands
- SAM, GTA, ZN
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NSP16 protein | protein | 290 | 30% helix, 21% strand | K0BWD0 |
| B | NSP10 protein | protein | 120 | 27% helix, 14% strand | K4LC41 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.52 | 0.75 | 41 | SAM, GTA |
| 2 | 155 | 0.50 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1025 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5YNM · Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAM and 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 5YNM · PDBe 5YNM · UniProt K0BWD0 · UniProt K4LC41
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