MolNFT v1 · #112647 · protein
2.1 a X-ray structure of fipv-3CLPRO bound to covalent inhibitor
4ZRO · 3C-like proteinase: “2.1 a X-ray structure of fipv-3CLPRO bound to covalent inhibitor”. X-ray diffraction, 2 ligands (BOC, CEV), 10 pockets (best druggability 0.82). MolNFT v1 #112647 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4ZRO
- Type
- protein
- Length
- 1,208 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Bounded inhibitor of N-(tert-butoxycarbonyl)-L-seryl-L…
- EC
- 3.4.22.-
- UniProt
- Q98VG9
- Ligands
- BOC, CEV
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3C-like proteinase (EC 3.4.22.-) | protein | 299 | 24% helix, 29% strand | Q98VG9 |
| E, F, G, H | Bounded inhibitor of N-(tert-butoxycarbonyl)-L-seryl-L- valyl-N-{(2S)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-YL]PENTAN-2- yl}-L-leucinamide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- BOC · Tert-butyl hydrogen carbonate · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- CEV · Ethyl (4R)-4-amino-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.82 | 0.86 | 90 | empty |
| 2 | 1009 | 0.77 | 0.79 | 95 | empty |
| 3 | 637 | 0.71 | 0.79 | 51 | empty |
| 4 | 444 | 0.70 | 0.81 | 55 | DMS |
| 5 | 454 | 0.67 | 0.79 | 57 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1200 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 818 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 694 Ų buried · 6 hydrogen bonds · protein-protein
- D–H · 296 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 293 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 4ZRO · 2.1 A X-Ray Structure of FIPV-3CLpro bound to covalent inhibitor · 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 Q98VG9
- Elsewhere: RCSB PDB 4ZRO · PDBe 4ZRO · UniProt Q98VG9
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