Research workbench
The structure of porcine epidemic diarrhea virus main protease in complex with an inhibitor
Analyse The structure of porcine epidemic diarrhea virus main protease in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GWZ
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pedv main protease; N-[(5-methylisoxazol-3-YL)CARBONYL]ALANYL-L-valyl-N~1~…
- EC
- 3.4.22.-
- UniProt
- P0C6V6
- Ligands
- 02J, PJE, 010
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Pedv main protease (EC 3.4.22.-) | protein | 299 | 24% helix, 29% strand | P0C6V6 |
| D, E | N-[(5-methylisoxazol-3-YL)CARBONYL]ALANYL-L-valyl-N~1~- ((1R,2Z)-4-(benzyloxy)-4-oxo-1-{[(3R)-2-oxopyrrolidin-3- YL]METHYL}BUT-2-enyl)-L-leucinamide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- 02J · 5-methyl-1,2-oxazole-3-carboxylic acid · ligand · 2 copies · chains B, D, A, E
- PJE · (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid · ligand · 2 copies · chains B, D, A, E
- 010 · phenylmethanol · ligand · 2 copies · chains B, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.74 | 0.77 | 92 | PJE, 010 |
| 2 | 359 | 0.64 | 0.79 | 59 | empty |
| 3 | 549 | 0.63 | 0.75 | 80 | empty |
| 4 | 81 | 0.39 | 0.78 | 18 | PJE, 010 |
Interfaces
3 interfaces between chains.
- B–A · 1031 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 319 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 293 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5GWZ · The structure of Porcine epidemic diarrhea virus main protease in complex with an… · 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 P0C6V6
- Elsewhere: RCSB PDB 5GWZ · PDBe 5GWZ · UniProt P0C6V6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.