MolNFT v1 · #180650 · protein + RNA
Crystal structure of SARS-cov-2 NSP16/10 heterodimer in complex with (M7GPPPA2M)PUPUPAPAPA (cap-1), S-adenosyl-L-homocysteine (sah) and two magnesium (mg) ions.
7L6T · 2'-O-methyltransferase: “Crystal structure of SARS-cov-2 NSP16/10 heterodimer in complex with (M7GPPPA2M)PUPUPAPAPA (cap-1)…”. X-ray diffraction, 7 ligands (M7G, SAH, BDF), 7 pockets (best druggability 0.61). MolNFT v1 #180650 on…
- PDB
- 7L6T
- Type
- protein + RNA
- Length
- 416 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, MG, ZN, CL
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 299 | 28% helix, 22% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 114 | 25% helix, 15% strand | P0DTD1 |
| C | RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*UP*A)-3') | rna | 3 | — | — |
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 · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.61 | 0.80 | 45 | SAH, GLC |
| 2 | 105 | 0.46 | 0.79 | 20 | empty |
| 3 | 59 | 0.37 | 0.79 | 15 | M7G |
| 4 | 52 | 0.34 | 0.79 | 13 | empty |
| 5 | 84 | 0.33 | 0.74 | 23 | FMT |
Interfaces
2 interfaces between chains.
- A–B · 943 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 569 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 7L6T · Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with… · the same entry in another collection · chain B against B, 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 7L6T · PDBe 7L6T · UniProt P0DTD1
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