Research workbench
Coxsackievirus B3 polymerase elongation complex (R2+1_FORM)
Analyse Coxsackievirus B3 polymerase elongation complex (R2+1_FORM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K4Y
- Type
- protein + RNA
- Length
- 1,990 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase; RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*…
- UniProt
- Q66338
- Ligands
- DCT
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | RNA-dependent RNA polymerase | protein | 463 | 42% helix, 15% strand | Q66338 |
| B, J | RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP* AP*A)-3') | rna | 18 | — | — |
| C, G, K, O | DNA/RNA (5'- R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(DOC))-3') | rna | 12 | — | — |
| D, H, L, P | RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') | rna | 5 | — | — |
| F, N | RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP* AP*A)-3') | rna | 17 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · 4 copies · chains A, B, C, E, F, G, I, J, K, M, N, O
- GOL · Glycerol · additive · 12 copies · chains A, E, I, M
- ACT · Acetate ion · additive · 3 copies · chains A, E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.83 | 0.85 | 81 | DCT, GOL |
| 2 | 1081 | 0.83 | 0.85 | 86 | DCT |
| 3 | 1195 | 0.83 | 0.85 | 111 | DCT |
| 4 | 1092 | 0.83 | 0.85 | 73 | DCT, GOL |
| 5 | 875 | 0.78 | 0.80 | 68 | GOL |
Interfaces
27 interfaces between chains.
- A–B · 1244 Ų buried · 29 hydrogen bonds · protein-nucleic
- I–J · 1244 Ų buried · 29 hydrogen bonds · protein-nucleic
- M–N · 1236 Ų buried · 26 hydrogen bonds · protein-nucleic
- E–F · 1233 Ų buried · 28 hydrogen bonds · protein-nucleic
- I–K · 745 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4K4Y · Coxsackievirus B3 polymerase elongation complex (r2+1_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 Q66338
- Elsewhere: RCSB PDB 4K4Y · PDBe 4K4Y · UniProt Q66338
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