Research workbench
Crystal structure of the enterovirus 71 polymerase elongation complex (C2S6M form)
Analyse Crystal structure of the enterovirus 71 polymerase elongation complex (C2S6M… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LSH
- Type
- protein + RNA
- Length
- 482 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
- E5RPG3
- Ligands
- ZN, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 2.7.7.48) | protein | 463 | 41% helix, 16% strand | E5RPG3 |
| B | RNA (35-mer) | rna | 10 | — | — |
| C | RNA (5'- R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*CP*C)-3') | rna | 9 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.79 | 0.83 | 48 | empty |
| 2 | 80 | 0.72 | 0.96 | 28 | empty |
| 3 | 175 | 0.69 | 0.88 | 28 | empty |
| 4 | 270 | 0.68 | 0.84 | 26 | empty |
| 5 | 67 | 0.53 | 0.86 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 902 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 740 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 414 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 6LSH · Crystal structure of the enterovirus 71 polymerase elongation complex (C2S6M 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 6LSH · PDBe 6LSH · UniProt E5RPG3
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