MolNFT v1 · #109135 · protein + RNA
Crystal structure of HCV NS5B genotype 2A jfh-1 isolate with S15G E86Q E87Q C223H V321I mutations and DELTA8 beta hairpin loop deletion in complex with sofosbuvir diphosphate gs-607596, MN2+ and symmetrical primer template 5'-caaaauuu
4WTG · RNA primer template caaaauuu: “Crystal structure of HCV NS5B genotype 2A jfh-1 isolate with S15G E86Q E87Q C223H V321I mutations and DELTA8…”. X-ray diffraction, 3 ligands (6GS, MN, CL), 4 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 4WTG
- Type
- protein + RNA
- Length
- 547 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA primer template caaaauuu; RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- Q99IB8
- Ligands
- 6GS, MN, CL
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | RNA primer template caaaauuu | rna | 7 | — | — |
| P | RNA primer template caaaauuu | rna | 5 | — | — |
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 535 | 49% helix, 14% strand | Q99IB8 |
Ligands and binding sites
- 6GS · 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate) · 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 | 143 | 0.79 | 0.96 | 42 | empty |
| 2 | 1033 | 0.77 | 0.79 | 88 | MN, 6GS |
| 3 | 109 | 0.46 | 0.79 | 19 | empty |
| 4 | 132 | 0.46 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- T–A · 815 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–A · 583 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 238 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Compared structures
- 4WTG · 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 Q99IB8
- Elsewhere: RCSB PDB 4WTG · PDBe 4WTG · UniProt Q99IB8
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