Research workbench
Co-transcriptional capping machineries in SARS-cov-2 rtc: coupling of N7-methyltransferase and 3'-5' exoribonuclease with polymerase reveals mechanisms for capping and proofreading
Analyse Co-transcriptional capping machineries in SARS-cov-2 rtc: coupling of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EGQ
- Type
- protein + RNA
- Length
- 6,760 residues
- Chains
- 22
- 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, 3.6.4.12, 3.6.4.13, 3.1.13.-
- UniProt
- P0DTD1
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 13 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 926 | 41% helix, 16% strand | P0DTD1 |
| B, O | Non-structural protein 8 | protein | 187 | 54% helix, 14% strand | P0DTD1 |
| C, P | Non-structural protein 7 | protein | 72 | 76% helix, 0% strand | P0DTD1 |
| D, Q | Non-structural protein 8 | protein | 186 | 55% helix, 15% strand | P0DTD1 |
| E, R | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 588 | 27% helix, 23% strand | P0DTD1 |
| G, T | Non-structural protein 9 | protein | 113 | 12% helix, 46% strand | P0DTD1 |
| H | Non-structural protein 10 | protein | 131 | 25% helix, 12% strand | P0DTD1 |
| K | Proofreading exoribonuclease (EC 3.1.13.-) | protein | 523 | 23% helix, 20% strand | P0DTD1 |
| U | Non-structural protein 10 | protein | 130 | 29% helix, 14% strand | P0DTD1 |
| X | Proofreading exoribonuclease (EC 3.1.13.-) | protein | 524 | 22% helix, 17% strand | P0DTD1 |
| F, S | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 596 | 24% helix, 16% strand | P0DTD1 |
| I, L | Primer RNA | rna | 25 | — | — |
| J, M | Template RNA | rna | 33 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 26 copies · chains A, E, H, K, N, R, U, X, F, S
- MG · Magnesium ion · metal · 3 copies · chains K, X
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 | 986 | 0.84 | 0.85 | 93 | empty |
| 2 | 1054 | 0.81 | 0.83 | 88 | empty |
| 3 | 174 | 0.79 | 0.95 | 28 | empty |
| 4 | 160 | 0.79 | 0.95 | 27 | empty |
| 5 | 927 | 0.79 | 0.81 | 85 | empty |
Interfaces
58 interfaces between chains.
- N–O · 2579 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2504 Ų buried · 13 hydrogen bonds · protein-protein
- U–X · 2230 Ų buried · 12 hydrogen bonds · protein-protein
- H–K · 2220 Ų buried · 16 hydrogen bonds · protein-protein
- P–Q · 1368 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7EGQ · Co-transcriptional capping machineries in SARS-CoV-2 RTC: Coupling of… · 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 7EGQ · PDBe 7EGQ · UniProt P0DTD1
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