MolNFT v1 · #53453 · protein
Crystal structure of foot-and-mouth disease virus 3C protease in complex with a decameric peptide corresponding to the VP1-2A cleavage junction with a gln to glu substitution at P1
2WV5 · Picornain 3C: “Crystal structure of foot-and-mouth disease virus 3C protease in complex with a decameric peptide…”. X-ray diffraction, 1 ligand (ACE), 7 pockets (best druggability 0.77). MolNFT v1 #53453 on GenesisL1: 3D structure…
- PDB
- 2WV5
- Type
- protein
- Length
- 836 residues
- Chains
- 8
- 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
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Picornain 3C (EC 3.4.22.28) | protein | 200 | 15% helix, 53% strand | P03306 |
| E, F, G, H | 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 · 4 copies · chains A, E, B, F, G, C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.77 | 0.80 | 81 | empty |
| 2 | 476 | 0.67 | 0.78 | 64 | empty |
| 3 | 237 | 0.54 | 0.77 | 31 | ACE |
| 4 | 120 | 0.48 | 0.79 | 29 | empty |
| 5 | 82 | 0.47 | 0.81 | 25 | empty |
Interfaces
10 interfaces between chains.
- D–H · 780 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 779 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 768 Ų buried · 19 hydrogen bonds · protein-protein
- C–G · 763 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 617 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2WV5 · Crystal structure of foot-and-mouth disease virus 3C protease in complex with a decameric… · 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 P03306
- Every structure of UniProt Q65050
- Elsewhere: RCSB PDB 2WV5 · PDBe 2WV5 · UniProt P03306 · UniProt Q65050
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