MolNFT v1 · #136115 · protein + RNA
Crystal structure of HCV NS5B genotype 2A jfh-1 isolate with S15G E86Q E87Q C223H V321I mutations and DELTA8 neta hairpoin loop deletion in complex with gs-639476 (diphsohate version of gs-9813), MN2+ and symmetrical primer template 5'-auaaauuu
5UJ2 · RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3'): “Crystal structure of HCV NS5B genotype 2A jfh-1 isolate with S15G E86Q E87Q C223H V321I mutations and DELTA8…”. X-ray diffraction, 3 ligands (8B4, MN, CL), 4 pockets (best druggability 0.77).…
- PDB
- 5UJ2
- Type
- protein + RNA
- Length
- 546 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3'); Genome polyprotein
- UniProt
- R9TEU1
- Ligands
- 8B4, MN, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3') | rna | 7 | — | — |
| P | RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3') | rna | 5 | — | — |
| A | Genome polyprotein | protein | 534 | 50% helix, 14% strand | R9TEU1 |
Ligands and binding sites
- 8B4 · (1S)-1-(4-aminoimidazo[2,1-f][1,2,4]triazin-7-yl)-1,4-anhydro-2-deoxy-2-fluoro-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-2-methyl-D-ribitol · ligand · chains T, P, A
- MN · Manganese (II) ion · metal · 3 copies · chains P, A
- CL · Chloride 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.77 | 0.79 | 96 | MN, 8B4 |
| 2 | 230 | 0.74 | 0.89 | 39 | empty |
| 3 | 140 | 0.47 | 0.78 | 27 | empty |
| 4 | 61 | 0.29 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- T–A · 766 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–A · 541 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 235 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 5UJ2 · Crystal structure of HCV NS5B genotype 2A JFH-1 isolate with S15G E86Q E87Q C223H V321I… · the same entry in another collection · chain T against T, 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 R9TEU1
- Elsewhere: RCSB PDB 5UJ2 · PDBe 5UJ2 · UniProt R9TEU1
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