Research workbench
Pestivirus NS3 helicase
Analyse Pestivirus NS3 helicase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CBG
- Type
- protein
- Length
- 1,854 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease NS3
- EC
- 3.4.21.113, 3.6.1.15, 3.6.4.13
- UniProt
- P19712
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease NS3 (EC 3.4.21.113, 3.6.1.15, 3.6.4.13) | protein | 459 | 38% helix, 21% strand | P19712 |
| B | Serine protease NS3 (EC 3.4.21.113, 3.6.1.15, 3.6.4.13) | protein | 460 | 37% helix, 20% strand | P19712 |
| C | Serine protease NS3 (EC 3.4.21.113, 3.6.1.15, 3.6.4.13) | protein | 465 | 37% helix, 20% strand | P19712 |
| D | Serine protease NS3 (EC 3.4.21.113, 3.6.1.15, 3.6.4.13) | protein | 470 | 36% helix, 20% strand | P19712 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.81 | 0.82 | 132 | ACT |
| 2 | 891 | 0.77 | 0.80 | 93 | ACT |
| 3 | 572 | 0.72 | 0.80 | 71 | empty |
| 4 | 622 | 0.72 | 0.79 | 73 | empty |
| 5 | 190 | 0.65 | 0.85 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1291 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 487 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 119 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 76 modified (engineered).
Compared structures
- 4CBG · Pestivirus NS3 helicase · 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 P19712
- Elsewhere: RCSB PDB 4CBG · PDBe 4CBG · UniProt P19712
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