Research workbench
Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P63)
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
- 4RF1
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Homo sapiens; Human betacoronavirus 2c Jordan-N3/2012
- Molecule
- ORF1ab protein; Ubiquitin-60S ribosomal protein L40
- UniProt
- M4STU1, P62987
- Ligands
- 3CN, ZN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.15 · 2 distinct chains · 25% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF1ab protein | protein | 319 | 26% helix, 38% strand | M4STU1 |
| B | Ubiquitin-60S ribosomal protein L40 | protein | 75 | 20% helix, 35% strand | P62987 |
Ligands and binding sites
- 3CN · 3-aminopropane · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- PGO · S-1,2-propanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.73 | 0.78 | 93 | PGO |
| 2 | 124 | 0.44 | 0.76 | 19 | PGO |
Interfaces
1 interface between chains.
- A–B · 852 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4RF1 · 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
- P62987 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P62987) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 M4STU1
- Every structure of UniProt P62987
- Elsewhere: RCSB PDB 4RF1 · PDBe 4RF1 · UniProt M4STU1 · UniProt P62987
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