Research workbench
Crystal structure of foot-and-mouth disease virus 3C protease in complex with a decameric peptide corresponding to the VP1-2A cleavage junction
Analyse Crystal structure of foot-and-mouth disease virus 3C protease in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WV4
- Type
- protein
- Length
- 415 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Picornain 3C; Foot and mouth disease virus (serotype a) variant VP1 capsid protein
- EC
- 3.4.22.28
- UniProt
- P03306, Q65050
- Ligands
- ACE
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Picornain 3C (EC 3.4.22.28) | protein | 201 | 13% helix, 56% strand | P03306 |
| B | Picornain 3C (EC 3.4.22.28) | protein | 196 | 16% helix, 51% strand | P03306 |
| C, D | Foot and mouth disease virus (serotype a) variant VP1 capsid protein | protein | 9 | 0% helix, 44% strand | Q65050 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.56 | 0.75 | 55 | empty |
| 2 | 147 | 0.47 | 0.77 | 24 | empty |
| 3 | 96 | 0.44 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 813 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 783 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 468 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2WV4 · Crystal structure of foot-and-mouth disease virus 3C protease in complex with a decameric… · the same entry in another collection · chain B against B, 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 P03306
- Every structure of UniProt Q65050
- Elsewhere: RCSB PDB 2WV4 · PDBe 2WV4 · UniProt P03306 · UniProt Q65050
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