Research workbench
Crystal structure of West Nile Virus NS2B-NS3 protease in complex with a capped dipeptide boronate inhibitor
Analyse Crystal structure of West Nile Virus NS2B-NS3 protease in complex with a capped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IDK
- Type
- protein
- Length
- 613 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- West Nile virus
- Molecule
- Genome polyprotein,SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3
- 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
- P06935
- Ligands
- 6A8
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.5 · 3 distinct chains · 2% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein,SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3 (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 | 204 | 2% helix, 45% strand | P06935 |
| B | Genome polyprotein,SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3 (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 | 204 | 2% helix, 48% strand | P06935 |
| C | Genome polyprotein,SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3 (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 | 205 | 2% helix, 47% strand | P06935 |
Ligands and binding sites
- 6A8 · ((R)-1-((S)-3-(4-(aminomethyl)phenyl)-2-benzamidopropaneamido)-4-guanidinobutyl)boronic acid, cyclic double ester with glycerol · ligand · 3 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · chains B
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.67 | 0.79 | 39 | empty |
| 2 | 156 | 0.55 | 0.81 | 23 | empty |
| 3 | 185 | 0.54 | 0.79 | 26 | empty |
| 4 | 159 | 0.53 | 0.80 | 29 | empty |
| 5 | 239 | 0.49 | 0.75 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–C · 907 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 589 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 5IDK · Crystal structure of west nile virus NS2B-NS3 protease in complex with a capped dipeptide… · 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 P06935
- Elsewhere: RCSB PDB 5IDK · PDBe 5IDK · UniProt P06935
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