Research workbench
Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS- cov-2 polymerase reveals mechanisms for capping and proofreading
Analyse Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS- cov-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EIZ
- Type
- protein + RNA
- Length
- 3,367 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7…
- EC
- 2.7.7.48, 3.1.13.-
- UniProt
- P0DTD1, P0DTC1
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 11 distinct chains · 33% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 926 | 40% helix, 13% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 187 | 57% helix, 13% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 72 | 71% helix, 0% strand | P0DTC1 |
| D | Non-structural protein 8 | protein | 186 | 58% helix, 13% strand | P0DTD1 |
| G | Non-structural protein 9 | protein | 113 | 12% helix, 45% strand | P0DTD1 |
| H | Non-structural protein 10 | protein | 131 | 24% helix, 8% strand | P0DTD1 |
| I | Primer | rna | 25 | — | — |
| J | Template | rna | 27 | — | — |
| K | Proofreading exoribonuclease (EC 3.1.13.-) | protein | 523 | 20% helix, 16% strand | P0DTD1 |
| E | Helicase | protein | 587 | 24% helix, 16% strand | P0DTD1 |
| F | Helicase | protein | 590 | 27% helix, 17% strand | P0DTD1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.81 | 0.82 | 117 | empty |
| 2 | 216 | 0.81 | 0.95 | 28 | empty |
| 3 | 122 | 0.78 | 0.96 | 33 | empty |
| 4 | 1090 | 0.77 | 0.79 | 100 | empty |
| 5 | 133 | 0.76 | 0.94 | 25 | empty |
Interfaces
22 interfaces between chains.
- A–B · 2494 Ų buried · 11 hydrogen bonds · protein-protein
- H–K · 2368 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1326 Ų buried · 5 hydrogen bonds · protein-protein
- I–J · 1197 Ų buried · 177 hydrogen bonds · nucleic-nucleic
- A–J · 1118 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7EIZ · Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase… · 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
- Every structure of UniProt P0DTC1
- Elsewhere: RCSB PDB 7EIZ · PDBe 7EIZ · UniProt P0DTD1 · UniProt P0DTC1
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