Research workbench
Cryo-EM structure of the tetrameric form of SARS-cov-2 NSP10-NSP14 (E191A)-RNA complex
Analyse Cryo-EM structure of the tetrameric form of SARS-cov-2 NSP10-NSP14 (E191A)-RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N0D
- Type
- protein + RNA
- Length
- 2,648 residues
- Chains
- 14
- 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
- 1N7, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 26% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Non-structural protein 10 | protein | 131 | 30% helix, 15% strand | P0DTD1 |
| B, D, F, H | Proofreading exoribonuclease (EC 3.1.13.-) | protein | 512 | 24% helix, 22% strand | P0DTD1 |
| T, I | RNA (5'- R(*GP*GP*GP*GP*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*G)-3') | rna | 19 | — | — |
| K, L | RNA (5'-R(*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') | rna | 14 | — | — |
| P, J | RNA (5'-R(*CP*CP*CP*CP*C)-3') | rna | 5 | — | — |
Ligands and binding sites
- 1N7 · Chapso · ligand · 2 copies · chains D, F, B, H
- ZN · Zinc ion · metal · 20 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 6 copies · chains B, K, D, P, F, L, H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.86 | 0.88 | 98 | empty |
| 2 | 1194 | 0.84 | 0.86 | 107 | empty |
| 3 | 1162 | 0.81 | 0.82 | 93 | 1N7 |
| 4 | 1170 | 0.80 | 0.81 | 90 | 1N7 |
| 5 | 411 | 0.75 | 0.85 | 47 | MG |
Interfaces
35 interfaces between chains.
- G–H · 2294 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2291 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2235 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2232 Ų buried · 25 hydrogen bonds · protein-protein
- B–H · 976 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7N0D · Cryo-EM structure of the tetrameric form of SARS-CoV-2 nsp10-nsp14 (E191A)-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 7N0D · PDBe 7N0D · UniProt P0DTD1
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