MolNFT v1 · #140221 · protein
Crystal structure of SARS coronavirus papain-like protease conjugated with beta-mercaptoethanol
5Y3Q · Replicase polyprotein 1A: “Crystal structure of SARS coronavirus papain-like protease conjugated with beta-mercaptoethanol”. X-ray diffraction, 2 ligands (NA, ZN), 3 pockets (best druggability 0.45). MolNFT v1 #140221 on GenesisL1…
- PDB
- 5Y3Q
- Type
- protein
- Length
- 317 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1A
- EC
- 3.4.19.12, 3.4.22.69
- UniProt
- P0C6U8
- Ligands
- NA, ZN
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1A (EC 3.4.19.12, 3.4.22.69) | protein | 317 | 26% helix, 36% strand | P0C6U8 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- BME · Beta-mercaptoethanol · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.45 | 0.83 | 13 | empty |
| 2 | 69 | 0.37 | 0.78 | 20 | NA |
| 3 | 50 | 0.26 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5Y3Q · Crystal structure of SARS coronavirus papain-like protease conjugated with… · 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 P0C6U8
- Elsewhere: RCSB PDB 5Y3Q · PDBe 5Y3Q · UniProt P0C6U8
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