MolNFT v1 · #180186 · protein + RNA
Structure of SARS-cov-2 backtracked complex complex bound to NSP13 helicase - btc (local refinement)
7KRP · RNA-directed RNA polymerase: “Structure of SARS-cov-2 backtracked complex complex bound to NSP13 helicase - btc (local refinement)”. Electron microscopy, 4 ligands (1N7, ADP, ZN), 18 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 7KRP
- Type
- protein + RNA
- Length
- 1,446 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7; RNA…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- 1N7, ADP, ZN, MG
- Pockets
- 18 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 927 | 40% helix, 17% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 186 | 58% helix, 16% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 75 | 75% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 185 | 54% helix, 16% strand | P0DTD1 |
| P | RNA (37-mer) | rna | 37 | — | — |
| T | RNA (36-mer) | rna | 36 | — | — |
Ligands and binding sites
- 1N7 · Chapso · ligand · 3 copies · chains A, D
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.83 | 0.95 | 44 | empty |
| 2 | 847 | 0.75 | 0.80 | 45 | empty |
| 3 | 496 | 0.72 | 0.82 | 36 | empty |
| 4 | 650 | 0.64 | 0.75 | 44 | empty |
| 5 | 264 | 0.64 | 0.82 | 33 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2573 Ų buried · 13 hydrogen bonds · protein-protein
- P–T · 1598 Ų buried · 122 hydrogen bonds · nucleic-nucleic
- C–D · 1508 Ų buried · 5 hydrogen bonds · protein-protein
- A–T · 1109 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 983 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 7KRP · Structure of SARS-CoV-2 backtracked complex complex bound to nsp13 helicase - BTC (local… · 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 7KRP · PDBe 7KRP · UniProt P0DTD1
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