Research workbench
SARS-cov-2 replication-transcription complex bound to NSP13 helicase - NSP13(2)-rtc dimer
Analyse SARS-cov-2 replication-transcription complex bound to NSP13 helicase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RE3
- Type
- protein + RNA
- Length
- 5,248 residues
- Chains
- 16
- 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
- UniProt
- P0DTD1
- Ligands
- ADP, AF3, 1N7, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 927 | 40% helix, 15% strand | P0DTD1 |
| B, H | Non-structural protein 8 | protein | 186 | 60% helix, 16% strand | P0DTD1 |
| C, I | Non-structural protein 7 | protein | 75 | 68% helix, 0% strand | P0DTD1 |
| D, J | Non-structural protein 8 | protein | 185 | 56% helix, 17% strand | P0DTD1 |
| E, F, K, L | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 590 | 25% helix, 19% strand | P0DTD1 |
| P, Q | Product RNA | rna | 34 | — | — |
| T, U | Template RNA | rna | 37 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, L, E, F, G, K
- AF3 · Aluminum fluoride · ligand · 4 copies · chains E, F, K, L
- 1N7 · Chapso · ligand · 2 copies · chains A, D, E, G, J, K
- ZN · Zinc ion · metal · 16 copies · chains A, E, F, G, K, L
- MG · Magnesium ion · metal · 6 copies · chains A, E, F, G, K, L
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 | 928 | 0.82 | 0.84 | 87 | empty |
| 2 | 1160 | 0.82 | 0.83 | 110 | MG, AF3 |
| 3 | 856 | 0.81 | 0.84 | 73 | empty |
| 4 | 1145 | 0.81 | 0.82 | 117 | MG, AF3 |
| 5 | 136 | 0.80 | 0.98 | 22 | empty |
Interfaces
39 interfaces between chains.
- A–B · 2547 Ų buried · 14 hydrogen bonds · protein-protein
- H–G · 2515 Ų buried · 12 hydrogen bonds · protein-protein
- Q–U · 1565 Ų buried · 124 hydrogen bonds · nucleic-nucleic
- P–T · 1552 Ų buried · 124 hydrogen bonds · nucleic-nucleic
- I–J · 1413 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7RE3 · SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC dimer · 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 7RE3 · PDBe 7RE3 · UniProt P0DTD1
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