MolNFT v1 · #168155 · protein
1.95 ångström resolution crystal structure of NSP10 - NSP16 complex from SARS-cov-2
6W75 · 2'-O-methyltransferase: “1.95 ångström resolution crystal structure of NSP10 - NSP16 complex from SARS-cov-2”. X-ray diffraction, 3 ligands (SAM, NA, ZN), 17 pockets (best druggability 0.58). MolNFT v1 #168155 on GenesisL1: 3D…
- PDB
- 6W75
- Type
- protein
- Length
- 826 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
- SAM, NA, ZN
- Pockets
- 17 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2'-O-methyltransferase (EC 2.1.1.-) | protein | 297 | 28% 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 | 292 | 28% helix, 24% strand | P0DTD1 |
| D | Non-structural protein 10 | protein | 115 | 24% helix, 15% strand | P0DTD1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains B, D
- FMT · Formic acid · additive · 20 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.58 | 0.74 | 52 | empty |
| 2 | 337 | 0.56 | 0.75 | 40 | SAM, FMT |
| 3 | 183 | 0.49 | 0.77 | 24 | empty |
| 4 | 93 | 0.44 | 0.79 | 18 | empty |
| 5 | 148 | 0.43 | 0.75 | 29 | SAM, FMT |
Interfaces
4 interfaces between chains.
- C–D · 968 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 958 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 797 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 567 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6W75 · 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex from SARS-CoV-2 · the same entry in another collection · chain C against C, 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 6W75 · PDBe 6W75 · UniProt P0DTD1
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