Research workbench
Crystal structure of zika NS3 protease in complex with 4- guanidinomethyl-phenylacetyl-lys-lys-arg-H
Analyse Crystal structure of zika NS3 protease in complex with 4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZMS
- Type
- protein
- Length
- 778 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-lys-lys-arg-H
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- Q32ZE1, H8XX12
- Ligands
- 2UE
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 38 | 0% helix, 45% strand | Q32ZE1 |
| B, E, H, K | NS3 protease | protein | 155 | 3% helix, 46% strand | H8XX12 |
| F, I | 4-guanidinomethyl-phenylacetyl-lys-lys-arg-H | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 2UE · 1-[4-(2-oxoethyl)benzyl]guanidine · ligand · 2 copies · chains B, D, E, F, A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.62 | 0.76 | 52 | 2UE |
| 2 | 143 | 0.45 | 0.76 | 24 | empty |
| 3 | 133 | 0.44 | 0.76 | 22 | empty |
| 4 | 117 | 0.43 | 0.77 | 20 | empty |
| 5 | 113 | 0.41 | 0.76 | 23 | empty |
Interfaces
17 interfaces between chains.
- J–K · 2103 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 2056 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 2017 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2012 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 428 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 d-amino, 2 covalent (D-amino acid, covalent ligand).
Compared structures
- 5ZMS · Crystal structure of Zika NS3 protease in complex with… · 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 H8XX12
- Elsewhere: RCSB PDB 5ZMS · PDBe 5ZMS · UniProt Q32ZE1 · UniProt H8XX12
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