Research workbench
Crystal structure of HCV NS3/4A protease in complex with N-terminal product 5A5B
Analyse Crystal structure of HCV NS3/4A protease in complex with N-terminal product 5A5B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M5O
- Type
- protein
- Length
- 410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3/4A; Tedvvcc peptide
- EC
- 3.4.21.98
- UniProt
- A8DG50, B3TKQ3
- Ligands
- ACE, ZN, SO4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NS3/4A (EC 3.4.21.98) | protein | 198 | 13% helix, 43% strand | A8DG50 |
| C, D | Tedvvcc peptide | protein | 7 | 0% helix, 57% strand | B3TKQ3 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.49 | 0.73 | 36 | empty |
| 2 | 60 | 0.41 | 0.81 | 17 | empty |
| 3 | 85 | 0.40 | 0.79 | 23 | empty |
| 4 | 59 | 0.40 | 0.82 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 480 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 477 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 288 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3M5O · Crystal structure of HCV NS3/4A protease in complex with N-terminal product 5A5B · 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 A8DG50
- Every structure of UniProt B3TKQ3
- Elsewhere: RCSB PDB 3M5O · PDBe 3M5O · UniProt A8DG50 · UniProt B3TKQ3
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