Research workbench
Crystal structure of zika NS3 protease with 4-guanidinomethyl- phenylacetyl-arg-arg-arg-4-amidinobenzylamide
Analyse Crystal structure of zika NS3 protease with 4-guanidinomethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZOB
- Type
- protein
- Length
- 780 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease subunit NS2B; NS3 protease; 4-guanidinomethyl-phenylacetyl-arg-arg-arg-4…
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- Q32ZE1, A0A142IX72
- Ligands
- 2UE, 00S
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 39 | 0% helix, 51% strand | Q32ZE1 |
| B, D | NS3 protease | protein | 156 | 3% helix, 45% strand | A0A142IX72 |
| G, E | Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 38 | 0% helix, 42% strand | Q32ZE1 |
| H, F | NS3 protease | protein | 154 | 3% helix, 44% strand | A0A142IX72 |
| I, J | 4-guanidinomethyl-phenylacetyl-arg-arg-arg-4- amidinobenzylamide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- 2UE · 1-[4-(2-oxoethyl)benzyl]guanidine · ligand · 2 copies · chains B, C, I, A, D, J
- 00S · 4-(aminomethyl)benzenecarboximidamide · ligand · 2 copies · chains B, I, D, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.68 | 0.78 | 61 | 2UE |
| 2 | 127 | 0.40 | 0.74 | 24 | empty |
| 3 | 122 | 0.40 | 0.75 | 22 | empty |
| 4 | 107 | 0.40 | 0.76 | 23 | empty |
| 5 | 91 | 0.38 | 0.76 | 19 | empty |
Interfaces
16 interfaces between chains.
- E–F · 2086 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2068 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 2062 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2054 Ų buried · 33 hydrogen bonds · protein-protein
- B–H · 434 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5ZOB · Crystal structure of Zika NS3 protease with 4-guanidinomethyl-phenylacetyl-Arg-Arg-Arg-4-a… · 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
- Every structure of UniProt A0A142IX72
- Elsewhere: RCSB PDB 5ZOB · PDBe 5ZOB · UniProt Q32ZE1 · UniProt A0A142IX72
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