Research workbench
Crystal structure of Zika NS2B-NS3 protease with compound 9
Analyse Crystal structure of Zika NS2B-NS3 protease with compound 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KK4
- Type
- protein
- Length
- 200 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.74
- Source
- Zika virus; Zika virus (strain Mr 766)
- Molecule
- Serine protease subunit NS2B; NS3 protease
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
- UniProt
- Q32ZE1, A0A142IX72
- Ligands
- DE0
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · resolution 1.74 · 2 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 39 | 0% helix, 49% strand | Q32ZE1 |
| B | NS3 protease | protein | 161 | 4% helix, 46% strand | A0A142IX72 |
Ligands and binding sites
- DE0 · 1-[(9~{R},16~{S},19~{S})-16,19-bis(4-azanylbutyl)-4,8, 15,18,21-pentakis(oxidanylidene)-3,7,14,17,20-pentazabicyclo[21.3.1]heptacosa-1(26),23(27),24-trien-9-yl]guanidine · ligand · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.38 | 0.74 | 24 | GOL |
Interfaces
1 interface between chains.
- A–B · 2034 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6KK4 · Crystal structure of zika NS2B-NS3 protease with compound 9 · 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 Q32ZE1
- Every structure of UniProt A0A142IX72
- Elsewhere: RCSB PDB 6KK4 · PDBe 6KK4 · UniProt Q32ZE1 · UniProt A0A142IX72
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