Research workbench
Crystal structure of the enterovirus 71 polymerase elongation complex (C3S6A/C3S6B form)
Analyse Crystal structure of the enterovirus 71 polymerase elongation complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LSE
- Type
- protein + RNA
- Length
- 480 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Human enterovirus 71; SYNTHETIC CONSTRUCT
- 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
- E5RPG3
- Ligands
- POP, ZN, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.25 · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 2.7.7.48) | protein | 464 | 41% helix, 15% strand | E5RPG3 |
| B | RNA (35-mer) | rna | 8 | — | — |
| 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 | 8 | — | — |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A, C
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · 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 | 939 | 0.80 | 0.82 | 95 | SO4, POP |
| 2 | 225 | 0.73 | 0.88 | 32 | empty |
| 3 | 82 | 0.53 | 0.85 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 929 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 670 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 322 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Compared structures
- 6LSE · Crystal structure of the enterovirus 71 polymerase elongation complex (C3S6A/C3S6B 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 E5RPG3
- Elsewhere: RCSB PDB 6LSE · PDBe 6LSE · UniProt E5RPG3
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