MolNFT v1 · #118652 · protein + RNA
Enterovirus 71 polymerase elongation complex (C3S1 form)
5F8L · Genome polyprotein: “Enterovirus 71 polymerase elongation complex (C3S1 form)”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.83). MolNFT v1 #118652 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5F8L
- Type
- protein + RNA
- Length
- 484 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; RNA (35-mer); RNA (5'- R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP…
- EC
- 2.7.7.48
- UniProt
- E5RPG2
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 2.7.7.48) | protein | 462 | 42% helix, 15% strand | E5RPG2 |
| B | RNA (35-mer) | rna | 12 | — | — |
| C | RNA (5'- R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*CP*C)-3') | rna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.83 | 0.84 | 80 | empty |
| 2 | 204 | 0.69 | 0.87 | 32 | empty |
| 3 | 68 | 0.50 | 0.85 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1000 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 683 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 454 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 5F8L · Enterovirus 71 Polymerase Elongation Complex (C3S1 Form) · 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 E5RPG2
- Elsewhere: RCSB PDB 5F8L · PDBe 5F8L · UniProt E5RPG2
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