Research workbench
Crystal structure of EV71 3C proteinase in complex with compound xb
Analyse Crystal structure of EV71 3C proteinase in complex with compound xb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C1U
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C proteinase
- EC
- 3.4.22.28
- UniProt
- A9XG43
- Ligands
- GHV
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C proteinase (EC 3.4.22.28) | protein | 181 | 12% helix, 54% strand | A9XG43 |
Ligands and binding sites
- GHV · (2S)-2-[[(E)-3-[4-(dimethylamino)phenyl]prop-2-enoyl]amino]-N-[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-phenyl-propanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.41 | 0.75 | 20 | empty |
| 2 | 120 | 0.37 | 0.73 | 22 | empty |
| 3 | 73 | 0.35 | 0.76 | 16 | empty |
| 4 | 63 | 0.30 | 0.75 | 22 | GHV |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5C1U · Crystal structure of EV71 3C Proteinase in complex with Compound Xb · 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 A9XG43
- Elsewhere: RCSB PDB 5C1U · PDBe 5C1U · UniProt A9XG43
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