MolNFT v1 · #122042 · protein
Crystal structure of west nile virus NS2B-NS3 protease in complex with a capped dipeptide boronate inhibitor
5IDK · Genome POLYPROTEIN,SERINE protease subunit NS2B, serine…: “Crystal structure of west nile virus NS2B-NS3 protease in complex with a capped dipeptide boronate inhibitor”. X-ray diffraction, 1 ligand (6A8), 7 pockets (best…
- PDB
- 5IDK
- Type
- protein
- Length
- 613 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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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