Research workbench
West nile VI rus NS2B-NS3PROTEASE in complexed with inhibitor naph-kkr-H
Analyse West nile VI rus NS2B-NS3PROTEASE in complexed with inhibitor naph-kkr-H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E90
- Type
- protein
- Length
- 428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS2B cofactor; NS3 protease
- EC
- 3.4.21.91
- Ligands
- NKK
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS2B cofactor | protein | 47 | 0% helix, 34% strand | — |
| B | NS3 protease (EC 3.4.21.91) | protein | 173 | 2% helix, 45% strand | — |
| C | NS2B cofactor | protein | 41 | 0% helix, 41% strand | — |
| D | NS3 protease (EC 3.4.21.91) | protein | 167 | 2% helix, 44% strand | — |
Ligands and binding sites
- NKK · N~2~-(naphthalen-2-ylcarbonyl)-L-lysyl-N-[(1S)-4-carbamimidamido-1-formylbutyl]-L-lysinamide · ligand · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.76 | 0.81 | 68 | NKK |
| 2 | 148 | 0.48 | 0.78 | 24 | empty |
| 3 | 125 | 0.47 | 0.79 | 19 | empty |
| 4 | 54 | 0.29 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2148 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2114 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 424 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 294 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 262 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3E90 · West Nile vi rus NS2B-NS3protease in complexed with inhibitor Naph-KKR-H · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 3E90 · PDBe 3E90
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