MolNFT v1 · #180648 · protein + RNA
Crystal structure of SARS-cov-2 NSP16/10 heterodimer in complex with (M7GPPPA2M)PUPUPAPAPA (cap-1), S-adenosyl-L-homocysteine (sah) and manganese (mn).
7L6R · 2'-O-methyltransferase: “Crystal structure of SARS-cov-2 NSP16/10 heterodimer in complex with (M7GPPPA2M)PUPUPAPAPA (cap-1)…”. X-ray diffraction, 8 ligands (M7G, SAH, BDF), 6 pockets (best druggability 0.57). MolNFT v1 #180648 on…
- PDB
- 7L6R
- Type
- protein + RNA
- Length
- 413 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'-O-methyltransferase; Non-structural protein 10; RNA…
- EC
- 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- M7G, SAH, BDF, GLC, MN, ZN, CL, SO4
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 300 | 29% helix, 22% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 109 | 26% helix, 16% strand | P0DTD1 |
| C | RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*UP*AP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · chains A, C
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, C
- BDF · beta-D-fructopyranose · ligand · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, C
- MN · Manganese (II) ion · metal · chains A, C
- ZN · Zinc ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · 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 | 212 | 0.57 | 0.80 | 38 | SAH, GLC |
| 2 | 100 | 0.43 | 0.78 | 20 | empty |
| 3 | 61 | 0.40 | 0.80 | 14 | M7G |
| 4 | 116 | 0.36 | 0.73 | 22 | BDF |
| 5 | 53 | 0.34 | 0.78 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 944 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 593 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 7L6R · Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer 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 P0DTD1
- Elsewhere: RCSB PDB 7L6R · PDBe 7L6R · UniProt P0DTD1
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