Research workbench
Coxsackievirus B3 polymerase elongation complex (R2_MG_FORM)
Analyse Coxsackievirus B3 polymerase elongation complex (R2_MG_FORM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K4Z
- Type
- protein + RNA
- Length
- 1,982 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*…
- EC
- 2.7.7.48
- UniProt
- Q66338
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 462 | 42% helix, 16% strand | Q66338 |
| B, 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 | — | — |
| C, G, K, O | RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3') | rna | 13 | — | — |
| D | RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') | rna | 2 | — | — |
| F, 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 | — | — |
| L, P | RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') | rna | 3 | — | — |
| H | RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, E, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.84 | 0.85 | 85 | MG |
| 2 | 1117 | 0.83 | 0.85 | 82 | MG |
| 3 | 1119 | 0.83 | 0.85 | 101 | MG |
| 4 | 1177 | 0.83 | 0.85 | 87 | MG |
| 5 | 1082 | 0.80 | 0.81 | 87 | empty |
Interfaces
27 interfaces between chains.
- M–N · 1242 Ų buried · 25 hydrogen bonds · protein-nucleic
- E–F · 1239 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 1234 Ų buried · 29 hydrogen bonds · protein-nucleic
- I–J · 1230 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–I · 840 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4K4Z · Coxsackievirus B3 polymerase elongation complex (r2_Mg_form) · the same entry in another collection · chain M against M, 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 4K4Z · PDBe 4K4Z · UniProt Q66338
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