Research workbench
X-ray structure of MERS coronavirus papain-like protease in complex with human ISG15
Analyse X-ray structure of MERS coronavirus papain-like protease in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BI8
- Type
- protein
- Length
- 824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1A; Ubiquitin-like protein ISG15
- UniProt
- K4LC41, P05161
- Ligands
- AYE, ZN
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ORF1A | protein | 259 | 27% helix, 39% strand | K4LC41 |
| C, D | Ubiquitin-like protein ISG15 | protein | 153 | 22% helix, 27% strand | P05161 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, C, B, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, D, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.75 | 0.83 | 57 | GOL, EDO |
| 2 | 469 | 0.72 | 0.81 | 56 | GOL |
| 3 | 234 | 0.69 | 0.85 | 32 | empty |
| 4 | 151 | 0.67 | 0.88 | 33 | empty |
| 5 | 273 | 0.66 | 0.82 | 51 | GOL |
Interfaces
4 interfaces between chains.
- B–D · 1219 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1215 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 709 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6BI8 · X-ray structure of MERS coronavirus papain-like protease in complex with human ISG15 · the same entry in another collection · chain A against A, TM-score 1.00
- P05161 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein ISG15 (P05161) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 K4LC41
- Every structure of UniProt P05161
- Elsewhere: RCSB PDB 6BI8 · PDBe 6BI8 · UniProt K4LC41 · UniProt P05161
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