Research workbench
Crystal structure of NS3/4A protease variant R155K in complex with mk- 5172
Analyse Crystal structure of NS3/4A protease variant R155K in complex with mk- 5172 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SUE
- Type
- protein
- Length
- 760 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 protease, NS4A protein
- UniProt
- A8DG50
- Ligands
- SUE, ZN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NS3 protease, NS4A protein | protein | 190 | 13% helix, 46% strand | A8DG50 |
Ligands and binding sites
- SUE · (1aR,5S,8S,10R,22aR)-5-tert-butyl-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-14-methoxy-3,6-di oxo-1,1a,3,4,5,6,9,10,18,19,20,21,22,22a-tetradecahydro-8H-7,10-methanocyclopropa[18,19][1,10,3,6]dioxadiazacyclononadec ino[11,12-b]quinoxaline-8-carboxamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.76 | 0.80 | 101 | empty |
| 2 | 539 | 0.64 | 0.76 | 79 | empty |
| 3 | 159 | 0.40 | 0.73 | 30 | empty |
| 4 | 106 | 0.36 | 0.74 | 24 | empty |
| 5 | 54 | 0.35 | 0.78 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 465 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 210 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 152 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3SUE · Crystal structure of NS3/4A protease variant R155K in complex with MK-5172 · 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
- Elsewhere: RCSB PDB 3SUE · PDBe 3SUE · UniProt A8DG50
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