Research workbench
Crystal structure of SARS-cov papain-like protease in complex with C- terminal domain mouse ISG15
Analyse Crystal structure of SARS-cov papain-like protease in complex with C- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TL7
- Type
- protein
- Length
- 781 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like protein ISG15; Replicase polyprotein 1AB
- EC
- 3.4.19.12, 3.4.22.69, 3.4.22.-, 2.7.7.48, 3.6.4.12, 3.6.4.13, 2.1.1.-, 3.1.13.-, 3.1.-.-
- UniProt
- Q64339, P0C6X7
- Ligands
- AYE, ZN
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ubiquitin-like protein ISG15 | protein | 76 | 25% helix, 36% strand | Q64339 |
| B | Replicase polyprotein 1AB (EC 3.4.19.12, 3.4.22.69, 3.4.22.-, 2.7.7.48, 3.6.4.12, 3.6.4.13, 2.1.1.-, 3.1.13.-, 3.1.-.-) | protein | 316 | 25% helix, 36% strand | P0C6X7 |
| D | Replicase polyprotein 1AB (EC 3.4.19.12, 3.4.22.69, 3.4.22.-, 2.7.7.48, 3.6.4.12, 3.6.4.13, 2.1.1.-, 3.1.13.-, 3.1.-.-) | protein | 313 | 27% helix, 36% strand | P0C6X7 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.72 | 0.80 | 48 | empty |
| 2 | 586 | 0.70 | 0.79 | 43 | empty |
| 3 | 174 | 0.53 | 0.79 | 20 | empty |
| 4 | 159 | 0.53 | 0.79 | 19 | empty |
| 5 | 172 | 0.50 | 0.78 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 984 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 894 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 144 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5TL7 · Crystal structure of SARS-CoV papain-like protease in complex with C-terminal domain… · the same entry in another collection · chain A against A, TM-score 1.00
- Q64339 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein ISG15 (Q64339) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q64339
- Every structure of UniProt P0C6X7
- Elsewhere: RCSB PDB 5TL7 · PDBe 5TL7 · UniProt Q64339 · UniProt P0C6X7
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