MolNFT v1 · #171268 · protein
The crystal structure of SARS-cov-2 NSP10-NSP16 methyltransferase complex with sinefungin
6YZ1: “The crystal structure of SARS-cov-2 NSP10-NSP16 methyltransferase complex with sinefungin”. X-ray diffraction, 2 ligands (SFG, ZN), 6 pockets (best druggability 0.51). MolNFT v1 #171268 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YZ1
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NSP16; NSP10
- EC
- 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- SFG, ZN
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NSP16 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 297 | 28% helix, 22% strand | P0DTD1 |
| B | NSP10 (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 113 | 26% helix, 15% strand | P0DTD1 |
Ligands and binding sites
- SFG · Sinefungin · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.51 | 0.75 | 37 | SFG |
| 2 | 102 | 0.44 | 0.78 | 19 | empty |
| 3 | 60 | 0.35 | 0.78 | 17 | empty |
| 4 | 51 | 0.32 | 0.77 | 13 | empty |
| 5 | 67 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 955 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6YZ1 · The crystal structure of SARS-CoV-2 nsp10-nsp16 methyltransferase complex with Sinefungin · 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 P0DTD1
- Elsewhere: RCSB PDB 6YZ1 · PDBe 6YZ1 · UniProt P0DTD1
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