MolNFT v1 · #120337 · protein
The structure of porcine epidemic diarrhea virus main protease in complex with an inhibitor
5GWZ · Pedv main protease: “The structure of porcine epidemic diarrhea virus main protease in complex with an inhibitor”. X-ray diffraction, 3 ligands (02J, PJE, 010), 4 pockets (best druggability 0.74). MolNFT v1 #120337 on GenesisL1: 3D…
- 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
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