Research workbench
Poliovirus polymerase elongation complex (R5_FORM)
Analyse Poliovirus polymerase elongation complex (R5_FORM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K4U
- Type
- protein + RNA
- Length
- 996 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase 3D-pol; RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*…
- EC
- 2.7.7.48
- UniProt
- P03300
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | RNA-directed RNA polymerase 3D-pol (EC 2.7.7.48) | protein | 462 | 40% helix, 16% strand | P03300 |
| B, F | RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP* GP*AP*AP*A)-3') | rna | 19 | — | — |
| C, G | RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*A)- 3') | rna | 15 | — | — |
| H, D | RNA (5'-R(P*GP*GP*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.82 | 0.86 | 68 | SO4 |
| 2 | 591 | 0.80 | 0.86 | 50 | SO4 |
| 3 | 108 | 0.76 | 0.96 | 23 | empty |
| 4 | 102 | 0.75 | 0.96 | 22 | empty |
| 5 | 223 | 0.73 | 0.88 | 35 | SO4 |
Interfaces
13 interfaces between chains.
- A–B · 1233 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 1226 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 721 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–G · 720 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 649 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Compared structures
- 4K4U · Poliovirus polymerase elongation complex (r5_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 P03300
- Elsewhere: RCSB PDB 4K4U · PDBe 4K4U · UniProt P03300
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