MolNFT v1 · #105771 · protein
Crystal structure of the middle-east respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P6522)
4RF0 · ORF1AB protein: “Crystal structure of the middle-east respiratory syndrome coronavirus papain-like protease in complex with…”. X-ray diffraction, 3 ligands (3CN, ZN, SO4), 4 pockets (best druggability 0.71). MolNFT v1 #105771 on…
- PDB
- 4RF0
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1AB protein; Ubiquitin-60S ribosomal protein L40
- UniProt
- M4STU1, P62987
- Ligands
- 3CN, ZN, SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF1AB protein | protein | 318 | 24% helix, 36% strand | M4STU1 |
| B | Ubiquitin-60S ribosomal protein L40 | protein | 75 | 20% helix, 33% strand | P62987 |
Ligands and binding sites
- 3CN · 3-aminopropane · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.71 | 0.79 | 63 | SO4 |
| 2 | 189 | 0.51 | 0.77 | 27 | empty |
| 3 | 133 | 0.47 | 0.78 | 23 | SO4 |
| 4 | 55 | 0.38 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1032 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4RF0 · 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 0.94
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 4RF0 · PDBe 4RF0 · UniProt M4STU1 · UniProt P62987
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