Research workbench
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 cdp, MN2+ and symmetrical primer template 5'-agaaauuu
Analyse Crystal structure of HCV NS5B genotype 2A jfh-1 isolate with S15G E86Q E87Q… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WTC
- Type
- protein + RNA
- Length
- 547 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA primer template agaaauuu; RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- Q99IB8
- Ligands
- CDP, MN, CL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | RNA primer template agaaauuu | rna | 8 | — | — |
| P | RNA primer template agaaauuu | rna | 5 | — | — |
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 534 | 49% helix, 14% strand | Q99IB8 |
Ligands and binding sites
- CDP · Cytidine-5'-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 | 285 | 0.78 | 0.90 | 53 | empty |
| 2 | 1071 | 0.77 | 0.79 | 89 | MN, CDP |
| 3 | 70 | 0.37 | 0.78 | 15 | empty |
| 4 | 81 | 0.35 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- T–A · 968 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–A · 547 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–P · 236 Ų buried · 16 hydrogen bonds · nucleic-nucleic
Compared structures
- 4WTC · 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 4WTC · PDBe 4WTC · UniProt Q99IB8
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