MolNFT v1 · #109133 · 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 GDP, MN2+ and symmetrical primer template 5'-acaaauuu
4WTE · RNA primer template acaaauuu: “Crystal structure of HCV NS5B genotype 2A jfh-1 isolate with S15G E86Q E87Q C223H V321I mutations and DELTA8…”. X-ray diffraction, 3 ligands (GDP, MN, CL), 4 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 4WTE
- Type
- protein + RNA
- Length
- 547 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA primer template acaaauuu; RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- Q99IB8
- Ligands
- GDP, MN, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | RNA primer template acaaauuu | rna | 7 | — | — |
| P | RNA primer template acaaauuu | rna | 5 | — | — |
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 535 | 49% helix, 15% strand | Q99IB8 |
Ligands and binding sites
- GDP · Guanosine-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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.77 | 0.79 | 95 | MN, GDP |
| 2 | 224 | 0.74 | 0.89 | 39 | empty |
| 3 | 52 | 0.68 | 0.97 | 17 | empty |
| 4 | 83 | 0.43 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- T–A · 788 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–A · 570 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–P · 242 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Compared structures
- 4WTE · 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 4WTE · PDBe 4WTE · UniProt Q99IB8
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