Research workbench
Crystal structure of coxsackievirus B3 3D polymerase in complex with gpc-N143
Analyse Crystal structure of coxsackievirus B3 3D polymerase in complex with gpc-N143 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y34
- Type
- protein
- Length
- 467 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3D polymerase
- UniProt
- Q5UEA2
- Ligands
- 45Z, SO4
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3D polymerase | protein | 467 | 41% helix, 15% strand | Q5UEA2 |
Ligands and binding sites
- 45Z · 2,2'-[(4-fluorobenzene-1,2-diyl)bis(oxy)]bis(5-nitrobenzonitrile) · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.74 | 0.78 | 101 | 45Z, SO4, GOL |
| 2 | 95 | 0.39 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 4Y34 · Crystal Structure of Coxsackievirus B3 3D polymerase in complex with GPC-N143 · 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 Q5UEA2
- Elsewhere: RCSB PDB 4Y34 · PDBe 4Y34 · UniProt Q5UEA2
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