Research workbench
Crystal structure of HCV NS5B 1B with (1,1-dioxo-2H-[1,2, 4]BENZOTHIADIAZIN-3-yl) AZOLO[1,5-A]PYRIMIDINE derivative
Analyse Crystal structure of HCV NS5B 1B with (1,1-dioxo-2H-[1,2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H98
- Type
- protein
- Length
- 1,110 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- P26663
- Ligands
- B5P
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 551 | 48% helix, 15% strand | P26663 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 559 | 48% helix, 15% strand | P26663 |
Ligands and binding sites
- B5P · N-{3-[5-hydroxy-8-(3-methylbutyl)-7-oxo-7,8-dihydroimidazo[1,2-a]pyrimidin-6-yl]-1,1-dioxido-4H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.80 | 0.81 | 85 | B5P, GOL |
| 2 | 1079 | 0.80 | 0.81 | 80 | B5P |
| 3 | 568 | 0.69 | 0.78 | 54 | empty |
| 4 | 266 | 0.67 | 0.83 | 27 | empty |
| 5 | 114 | 0.48 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 595 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3H98 · Crystal structure of HCV NS5b 1b with (1,1-dioxo-2H-[1,2,4]benzothiadiazin-3-yl)… · 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 P26663
- Elsewhere: RCSB PDB 3H98 · PDBe 3H98 · UniProt P26663
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