MolNFT v1 · #173546 · protein + RNA
Structure of elongating SARS-cov-2 RNA-dependent RNA polymerase with remdesivir at position -3 (structure 1)
7B3B · RNA-directed RNA polymerase NSP12: “Structure of elongating SARS-cov-2 RNA-dependent RNA polymerase with remdesivir at position -3 (structure 1)”. Electron microscopy, 2 ligands (F86, ZN), 13 pockets (best druggability 0.78). MolNFT…
- PDB
- 7B3B
- Type
- protein + RNA
- Length
- 1,012 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
- 13 · best druggability 0.78
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 | 39% helix, 25% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 62 | 85% helix, 0% strand | P0DTD1 |
| P | DNA/RNA (5'-R(P*CP*UP*AP*CP*GP*CP*G)-D(P*(RMP))-R(P*UP*G)- 3') | rna | 9 | — | — |
| T | RNA (5'-R(P*UP*GP*CP*AP*UP*CP*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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.78 | 0.86 | 51 | F86 |
| 2 | 383 | 0.74 | 0.85 | 43 | empty |
| 3 | 390 | 0.65 | 0.79 | 46 | empty |
| 4 | 198 | 0.53 | 0.78 | 37 | empty |
| 5 | 53 | 0.47 | 0.85 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2492 Ų buried · 15 hydrogen bonds · protein-protein
- A–T · 1088 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 866 Ų buried · 10 hydrogen bonds · protein-protein
- A–P · 576 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–T · 484 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7B3B · 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 7B3B · PDBe 7B3B · UniProt P0DTD1
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