Research workbench
Crystal structure of SARS-cov-2 NSP16/10 heterodimer in complex with (M7GPPPA)PUPUPAPAPA (cap-0) and S-adenosylmethionine (SAM).
Analyse Crystal structure of SARS-cov-2 NSP16/10 heterodimer in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JYY
- Type
- protein + RNA
- Length
- 847 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'-O-methyltransferase; Non-structural protein 10; RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3')
- EC
- 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- M7G, SAM, ZN, NA, MG, CL
- Pockets
- 20 · best druggability 0.56
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 300 | 28% helix, 23% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 129 | 25% helix, 13% strand | P0DTD1 |
| C | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 297 | 29% helix, 23% strand | P0DTD1 |
| D | Non-structural protein 10 | protein | 115 | 21% helix, 15% strand | P0DTD1 |
| E, F | RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · 2 copies · chains A, E, C, F
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, E, C, F
- ZN · Zinc ion · metal · 4 copies · chains B, D
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, E, C, F
- CL · Chloride ion · ion · chains A
- FMT · Formic acid · additive · 7 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.56 | 0.81 | 23 | SAM |
| 2 | 157 | 0.56 | 0.81 | 28 | SAM |
| 3 | 244 | 0.49 | 0.74 | 36 | empty |
| 4 | 162 | 0.48 | 0.77 | 23 | empty |
| 5 | 167 | 0.46 | 0.75 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–B · 962 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 961 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 840 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 779 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 571 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7JYY · Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA… · the same entry in another collection · chain D against D, 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 7JYY · PDBe 7JYY · UniProt P0DTD1
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