MolNFT v1 · #180493 · protein + RNA
SARS-cov-2 rdrp in complex with 4 remdesivir monophosphate
7L1F · RNA-directed RNA polymerase: “SARS-cov-2 rdrp in complex with 4 remdesivir monophosphate”. Electron microscopy, 1 ligand (F86), 20 pockets (best druggability 0.78). MolNFT v1 #180493 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7L1F
- Type
- protein + RNA
- Length
- 1,040 residues
- Chains
- 5
- 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
- F86
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 39% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 832 | 37% helix, 11% strand | P0DTD1 |
| C | Non-structural protein 8 | protein | 114 | 35% helix, 23% strand | P0DTD1 |
| D | Non-structural protein 7 | protein | 63 | 71% helix, 0% strand | P0DTD1 |
| P | RNA (5'-R(P*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*U*(F86) *(F86)*(F86)*(F86))-3') | rna | 13 | — | — |
| T | RNA (5'- R(P*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*G)-3') | rna | 18 | — | — |
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 · 4 copies · chains A, P, T
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 | 772 | 0.78 | 0.82 | 95 | empty |
| 2 | 1143 | 0.76 | 0.78 | 94 | F86 |
| 3 | 108 | 0.70 | 0.92 | 21 | empty |
| 4 | 71 | 0.68 | 0.95 | 22 | empty |
| 5 | 94 | 0.67 | 0.91 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2485 Ų buried · 16 hydrogen bonds · protein-protein
- A–T · 894 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 772 Ų buried · 9 hydrogen bonds · protein-protein
- P–T · 576 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–P · 271 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7L1F · SARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate · 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 7L1F · PDBe 7L1F · UniProt P0DTD1
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