Research workbench
Crystal structure of zika NS2B-NS3 protease with compound 2
Analyse Crystal structure of zika NS2B-NS3 protease with compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KK2
- Type
- protein
- Length
- 193 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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
- D9U
- Pockets
- 1 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% 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 | 38 | 0% helix, 47% strand | Q32ZE1 |
| B | NS3 protease | protein | 155 | 5% helix, 46% strand | A0A142IX72 |
Ligands and binding sites
- D9U · 1-[(10~{S},17~{S},20~{S})-17,20-bis(4-azanylbutyl)-4,9, 16,19,22-pentakis(oxidanylidene)-3,8,15,18,21-pentazabicyclo[22.2.2]octacosa-1(27),24(28),25-trien-10-yl]guanidine · ligand · chains A, 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 | 141 | 0.44 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2062 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6KK2 · Crystal structure of Zika NS2B-NS3 protease with compound 2 · 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 6KK2 · PDBe 6KK2 · UniProt Q32ZE1 · UniProt A0A142IX72
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