MolNFT v1 · #176644 · protein + RNA
SARS-cov-2 rdrp catalytic complex with T33-1 RNA
7DTE · RNA-directed RNA polymerase: “SARS-cov-2 rdrp catalytic complex with T33-1 RNA”. Electron microscopy, 1 ligand (ZN), 17 pockets (best druggability 0.80). MolNFT v1 #176644 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7DTE
- Type
- protein + RNA
- Length
- 1,436 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
- ZN
- Pockets
- 17 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 928 | 43% helix, 16% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 187 | 55% helix, 16% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 73 | 70% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 186 | 52% helix, 15% strand | P0DTD1 |
| F | RNA (57-mer) | rna | 33 | — | — |
| G | RNA (33-mer) | rna | 29 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.80 | 0.96 | 29 | empty |
| 2 | 1074 | 0.78 | 0.81 | 72 | empty |
| 3 | 493 | 0.72 | 0.82 | 31 | empty |
| 4 | 905 | 0.70 | 0.76 | 47 | empty |
| 5 | 476 | 0.70 | 0.80 | 51 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2542 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1395 Ų buried · 3 hydrogen bonds · protein-protein
- F–G · 1358 Ų buried · 111 hydrogen bonds · nucleic-nucleic
- A–F · 1084 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 926 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7DTE · SARS-CoV-2 RdRP catalytic complex with T33-1 RNA · 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 7DTE · PDBe 7DTE · UniProt P0DTD1
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