Research workbench
Crystal structure of SARS-cov-2 NSP16/10 heterodimer apo-form.
Analyse Crystal structure of SARS-cov-2 NSP16/10 heterodimer apo-form. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ULT
- Type
- protein
- Length
- 827 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2'-O-methyltransferase; Non-structural protein 10
- EC
- 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- NA, ZN
- Pockets
- 16 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 292 | 29% helix, 23% strand | P0DTD1 |
| B | Non-structural protein 10 | protein | 122 | 23% helix, 14% strand | P0DTD1 |
| C | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 298 | 28% helix, 22% strand | P0DTD1 |
| D | Non-structural protein 10 | protein | 115 | 24% helix, 15% strand | P0DTD1 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains B, D
- FMT · Formic acid · additive · 17 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.59 | 0.73 | 61 | FMT |
| 2 | 287 | 0.55 | 0.76 | 51 | NA, FMT |
| 3 | 188 | 0.48 | 0.76 | 29 | empty |
| 4 | 85 | 0.41 | 0.78 | 19 | NA |
| 5 | 109 | 0.40 | 0.76 | 23 | FMT |
Interfaces
4 interfaces between chains.
- A–B · 964 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 948 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 876 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 576 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7ULT · Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer Apo-Form. · 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 7ULT · PDBe 7ULT · UniProt P0DTD1
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