Research workbench
Co-complex of the of NS3-4A protease with the inhibitory peptide CP5- 46-a (in-house data)
Analyse Co-complex of the of NS3-4A protease with the inhibitory peptide CP5- 46-a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A1T
- Type
- protein
- Length
- 422 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nonstructural protein 4A, serine protease NS3; CP5-46-a peptide
- EC
- 3.4.21.98, 3.6.1.15, 3.6.4.13
- UniProt
- P26662
- Ligands
- BCT, K, ZN, CL
- Pockets
- 2 · best druggability 0.26
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nonstructural protein 4A, serine protease NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 193 | 14% helix, 46% strand | P26662 |
| B | Nonstructural protein 4A, serine protease NS3 (EC 3.4.21.98, 3.6.1.15, 3.6.4.13) | protein | 194 | 13% helix, 45% strand | P26662 |
| C | CP5-46-a peptide | protein | 17 | 0% helix, 24% strand | — |
| D | CP5-46-a peptide | protein | 18 | 0% helix, 22% strand | — |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.26 | 0.73 | 11 | empty |
| 2 | 56 | 0.26 | 0.73 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–C · 950 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 940 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4A1T · Co-Complex of the of NS3-4A protease with the inhibitory peptide CP5- 46-A (in-House data) · 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 P26662
- Elsewhere: RCSB PDB 4A1T · PDBe 4A1T · UniProt P26662
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