Research workbench
West nile virus NS2B/NS3PROTEASE in complex with bz-nle-lys-arg-arg-H
Analyse West nile virus NS2B/NS3PROTEASE in complex with bz-nle-lys-arg-arg-H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FP7
- Type
- protein
- Length
- 190 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; N-benzoyl-L-norleucyl-L-lysyl-N-[(2S)-5-carbamimidamido-1…
- 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
- BEZ, OAR
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (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 | 40 | 0% helix, 43% strand | P06935 |
| B | Genome polyprotein (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 | 147 | 5% helix, 48% strand | P06935 |
| C | N-benzoyl-L-norleucyl-L-lysyl-N-[(2S)-5-carbamimidamido-1- hydroxypentan-2-yl]-L-argininamide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains B, C
- OAR · N-(4-amino-5-hydroxy-pentyl)-guanidine · ligand · chains B, C
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 | 157 | 0.50 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2133 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 268 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 128 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2FP7 · West Nile Virus NS2B/NS3protease in complex with Bz-Nle-Lys-Arg-Arg-H · 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 2FP7 · PDBe 2FP7 · UniProt P06935
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