MolNFT v1 · #173547 · protein + RNA
Structure of elongating SARS-cov-2 RNA-dependent RNA polymerase with remdesivir at position -4 (structure 2)
7B3C · RNA-directed RNA polymerase NSP12: “Structure of elongating SARS-cov-2 RNA-dependent RNA polymerase with remdesivir at position -4 (structure 2)”. Electron microscopy, 2 ligands (F86, ZN), 10 pockets (best druggability 0.84). MolNFT…
- PDB
- 7B3C
- Type
- protein + RNA
- Length
- 1,013 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase NSP12; Non-structural protein 8; Non-structural protein 7…
- EC
- 2.7.7.48
- UniProt
- P0DTD1
- Ligands
- F86, ZN
- Pockets
- 10 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase NSP12 (EC 2.7.7.48) | protein | 814 | 45% helix, 15% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 115 | 38% helix, 25% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 62 | 87% helix, 0% strand | P0DTD1 |
| P | DNA/RNA (5'-R(P*CP*UP*AP*CP*GP*CP*A)-D(P*(RMP))- R(P*GP*UP*G)-3') | rna | 10 | — | — |
| T | RNA (5'-R(P*UP*CP*AP*CP*UP*UP*GP*CP*GP*UP*AP*G)-3') | rna | 12 | — | — |
Ligands and binding sites
- F86 · [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-F][1, 2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · chains A, P, T
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.84 | 0.86 | 92 | F86 |
| 2 | 508 | 0.68 | 0.79 | 66 | empty |
| 3 | 51 | 0.55 | 0.90 | 19 | empty |
| 4 | 64 | 0.52 | 0.86 | 19 | empty |
| 5 | 176 | 0.47 | 0.76 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2477 Ų buried · 14 hydrogen bonds · protein-protein
- A–T · 1109 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 866 Ų buried · 8 hydrogen bonds · protein-protein
- A–P · 750 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 518 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7B3C · Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with Remdesivir at… · 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 7B3C · PDBe 7B3C · UniProt P0DTD1
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