Research workbench
Cryo-EM structure of the monomeric form of SARS-cov-2 NSP10-NSP14 (E191A)-RNA complex
Analyse Cryo-EM structure of the monomeric 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
- 7N0C
- Type
- protein + RNA
- Length
- 693 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 10; Proofreading exoribonuclease; RNA (25-mer); RNA (24-mer)
- EC
- 3.1.13.-
- UniProt
- P0DTD1
- Ligands
- ZN, MG
- Pockets
- 7 · best druggability 0.73
Structure
electron microscopy · 4 distinct chains · 21% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 10 | protein | 131 | 24% helix, 14% strand | P0DTD1 |
| B | Proofreading exoribonuclease (EC 3.1.13.-) | protein | 513 | 20% helix, 21% strand | P0DTD1 |
| T | RNA (25-mer) | rna | 25 | — | — |
| D | RNA (24-mer) | rna | 24 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.73 | 0.79 | 56 | empty |
| 2 | 969 | 0.66 | 0.73 | 50 | empty |
| 3 | 248 | 0.57 | 0.79 | 25 | empty |
| 4 | 152 | 0.45 | 0.76 | 29 | empty |
| 5 | 140 | 0.44 | 0.76 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2324 Ų buried · 26 hydrogen bonds · protein-protein
- T–D · 1080 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- B–D · 504 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–T · 394 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–T · 86 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 7N0C · Cryo-EM structure of the monomeric 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 7N0C · PDBe 7N0C · UniProt P0DTD1
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