MolNFT v1 · #181964 · protein
Crystal structure of the SARS-cov-2 exon-NSP10 complex containing MG2+ ion
7MC6 · Proofreading exoribonuclease: “Crystal structure of the SARS-cov-2 exon-NSP10 complex containing MG2+ ion”. X-ray diffraction, 3 ligands (ZN, MG, CL), 3 pockets (best druggability 0.51). MolNFT v1 #181964 on GenesisL1: 3D structure…
- PDB
- 7MC6
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proofreading exoribonuclease; Non-structural protein 10
- EC
- 3.1.13.-
- UniProt
- P0DTD1
- Ligands
- ZN, MG, CL
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proofreading exoribonuclease (EC 3.1.13.-) | protein | 285 | 25% helix, 25% strand | P0DTD1 |
| M | Non-structural protein 10 | protein | 130 | 31% helix, 16% strand | P0DTD1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, M
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.51 | 0.79 | 28 | empty |
| 2 | 113 | 0.46 | 0.78 | 18 | empty |
| 3 | 135 | 0.40 | 0.74 | 23 | MG |
Interfaces
1 interface between chains.
- A–M · 2264 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7MC6 · Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex containing Mg2+ ion · 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 7MC6 · PDBe 7MC6 · UniProt P0DTD1
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