MolNFT v1 · #118653 · protein + RNA
Enterovirus 71 polymerase elongation complex (C3S4/5 form)
5F8M · Genome polyprotein: “Enterovirus 71 polymerase elongation complex (C3S4/5 form)”. X-ray diffraction, 4 ligands (POP, MG, ZN), 5 pockets (best druggability 0.80). MolNFT v1 #118653 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5F8M
- 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
- POP, MG, ZN, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 2.7.7.48) | protein | 462 | 42% helix, 16% 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*CP*U)-3') | rna | 10 | — | — |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.80 | 0.82 | 78 | MG, POP |
| 2 | 201 | 0.73 | 0.89 | 31 | GOL |
| 3 | 61 | 0.51 | 0.86 | 15 | empty |
| 4 | 51 | 0.47 | 0.85 | 15 | empty |
| 5 | 53 | 0.39 | 0.81 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1064 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 910 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 475 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Compared structures
- 5F8M · Enterovirus 71 Polymerase Elongation Complex (C3S4/5 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 5F8M · PDBe 5F8M · UniProt E5RPG2
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