Research workbench
Crystal structure of unlinked NS2B-NS3 protease from zika virus in complex with inhibitor mi-2295
Analyse Crystal structure of unlinked NS2B-NS3 protease from zika virus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OC2
- Type
- protein
- Length
- 198 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease subunit NS2B; Serine protease NS3; Cyclic…
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- Q32ZE1
- Ligands
- V8N
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease subunit NS2B | protein | 39 | 0% helix, 46% strand | Q32ZE1 |
| B | Serine protease NS3 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 155 | 5% helix, 48% strand | Q32ZE1 |
| D | Cyclic 1[2-chloro-4-methoxy-phenyl-oxymethyl]-4-[2,6- dichloro-phenyl-oxymethyl]-benzene-(7-3)-7-benzyl-1,3-dimethyl-8- piperazin-1-yl-3,7-dihydro-purine-2,6-dione-(7-19)-N-acetyl-L- cysteine-(8-25)-[3R-[3A,4A,5B(S*)]]-5-(1-carboxy-1-phosphonoethoxy)- 4-hydroxy-3-(phosphonooxy)-1-cyclohexene-1-carboxylic acid-()-(6E, 11E)-heptadeca-6,11-diene-9,9-DIYLBIS(PHOSPHONIC acid) | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- V8N · 2-[3-(aminomethyl)phenyl]ethanoic acid · ligand · chains B, D
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 | 100 | 0.38 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1987 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 397 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 d-amino, 1 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 7OC2 · Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor… · 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
- Elsewhere: RCSB PDB 7OC2 · PDBe 7OC2 · UniProt Q32ZE1
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