MolNFT v1 · #180950 · protein
Crystal structure of the SARS cov-1 papain-like protease in complex with peptide inhibitor VIR251
7LFV: “Crystal structure of the SARS cov-1 papain-like protease in complex with peptide inhibitor VIR251”. X-ray diffraction, 6 ligands (73O, GVE, ZN), 3 pockets (best druggability 0.81). MolNFT v1 #180950 on GenesisL1: 3D structure…
- PDB
- 7LFV
- Type
- protein
- Length
- 630 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease; Papain-like protease peptide inhibitor VIR251
- EC
- 3.4.19.12, 3.4.22.-, 3.4.22.69
- UniProt
- P0C6U8
- Ligands
- 73O, GVE, ZN, SO4, NH4, CL
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Papain-like protease (EC 3.4.19.12, 3.4.22.-, 3.4.22.69) | protein | 312 | 26% helix, 37% strand | P0C6U8 |
| A | Papain-like protease (EC 3.4.19.12, 3.4.22.-, 3.4.22.69) | protein | 314 | 26% helix, 36% strand | P0C6U8 |
| D, F | Papain-like protease peptide inhibitor VIR251 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- 73O · (2~{S})-2-azanyl-4-(4-hydroxyphenyl)butanoic acid · ligand · 2 copies · chains A, D, B, F
- GVE · Methyl 4-aminobutanoate · ligand · 2 copies · chains A, D, B, F
- ZN · Zinc ion · metal · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 3 copies · chains B, A
- NH4 · Ammonium ion · ion · chains A
- CL · Chloride ion · ion · chains B, A
- EDO · 1,2-ethanediol · additive · 21 copies · chains B, A
- ACY · Acetic acid · additive · 2 copies · chains A, B, F
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 | 989 | 0.81 | 0.82 | 92 | EDO |
| 2 | 62 | 0.39 | 0.79 | 12 | EDO |
| 3 | 55 | 0.36 | 0.79 | 14 | ACY, 73O |
Interfaces
3 interfaces between chains.
- B–A · 1009 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 190 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 189 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 7LFV · Crystal structure of the SARS CoV-1 Papain-like protease in complex with peptide… · 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 P0C6U8
- Elsewhere: RCSB PDB 7LFV · PDBe 7LFV · UniProt P0C6U8
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