Research workbench
Crystal structure of the middle east respiratory syndrome coronavirus papain-like protease bound to ubiquitin variant ME.4
Analyse Crystal structure of the middle east respiratory syndrome coronavirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V69
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MERS-cov plpro; ME.4
- UniProt
- K0BWD0
- Ligands
- ZN, NA, CL
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MERS-cov plpro | protein | 322 | 25% helix, 38% strand | K0BWD0 |
| B | ME.4 | protein | 72 | 21% helix, 35% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PGO · S-1,2-propanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.64 | 0.80 | 48 | PGO |
| 2 | 282 | 0.58 | 0.77 | 42 | empty |
| 3 | 153 | 0.47 | 0.76 | 22 | NA |
Interfaces
1 interface between chains.
- A–B · 1070 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5V69 · Crystal structure of the Middle East respiratory syndrome coronavirus papain-like… · 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 K0BWD0
- Elsewhere: RCSB PDB 5V69 · PDBe 5V69 · UniProt K0BWD0
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