MolNFT v1 · #182670 · protein + RNA
Cryo-EM structure of SARS-cov-2 NSP10-NSP14 (wt)-RNA complex
7N0B · Non-structural protein 10: “Cryo-EM structure of SARS-cov-2 NSP10-NSP14 (wt)-RNA complex”. Electron microscopy, 2 ligands (ZN, CA), 6 pockets (best druggability 0.75). MolNFT v1 #182670 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7N0B
- Type
- protein + RNA
- Length
- 682 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 10; Proofreading exoribonuclease; RNA (5'…
- EC
- 3.1.13.-
- UniProt
- P0DTD1
- Ligands
- ZN, CA
- Pockets
- 6 · best druggability 0.75
Structure
electron microscopy · 4 distinct chains · 21% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 10 | protein | 131 | 27% helix, 12% strand | P0DTD1 |
| B | Proofreading exoribonuclease (EC 3.1.13.-) | protein | 512 | 20% helix, 21% strand | P0DTD1 |
| T | RNA (5'- R(*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*U)-3') | rna | 20 | — | — |
| D | RNA (5'- R(*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') | rna | 19 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.75 | 0.83 | 48 | empty |
| 2 | 302 | 0.62 | 0.80 | 28 | empty |
| 3 | 663 | 0.60 | 0.73 | 39 | empty |
| 4 | 179 | 0.51 | 0.78 | 28 | empty |
| 5 | 119 | 0.47 | 0.78 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2330 Ų buried · 25 hydrogen bonds · protein-protein
- T–D · 832 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- B–D · 492 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–T · 339 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–T · 66 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 7N0B · Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 (WT)-RNA complex · 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 7N0B · PDBe 7N0B · UniProt P0DTD1
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