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Structure of SARS-cov-2 backtracked complex bound to NSP13 helicase - NSP13(1)-btc
Analyse Structure of SARS-cov-2 backtracked 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
- 7KRN
- Type
- protein + RNA
- Length
- 2,043 residues
- Chains
- 7
- 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
- 1N7, ADP, AF3, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 927 | 37% helix, 15% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 186 | 56% helix, 12% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 75 | 69% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 185 | 50% helix, 17% strand | P0DTD1 |
| E | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 590 | 25% helix, 19% strand | P0DTD1 |
| P | RNA (37-mer) | rna | 37 | — | — |
| T | RNA (43-mer) | rna | 43 | — | — |
Ligands and binding sites
- 1N7 · Chapso · ligand · 3 copies · chains A, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, E
- AF3 · Aluminum fluoride · ligand · chains E
- ZN · Zinc ion · metal · 5 copies · chains A, E
- MG · Magnesium ion · metal · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.82 | 0.96 | 41 | empty |
| 2 | 272 | 0.78 | 0.90 | 48 | empty |
| 3 | 668 | 0.75 | 0.82 | 41 | empty |
| 4 | 491 | 0.73 | 0.82 | 38 | empty |
| 5 | 723 | 0.70 | 0.77 | 57 | empty |
Interfaces
17 interfaces between chains.
- A–B · 2535 Ų buried · 13 hydrogen bonds · protein-protein
- P–T · 1580 Ų buried · 129 hydrogen bonds · nucleic-nucleic
- C–D · 1532 Ų buried · 7 hydrogen bonds · protein-protein
- E–T · 1261 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–T · 1131 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 7KRN · Structure of SARS-CoV-2 backtracked complex bound to nsp13 helicase - nsp13(1)-BTC · 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 7KRN · PDBe 7KRN · UniProt P0DTD1
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