Research workbench
Crystal structure of HCV NS5B genotype 2A jfh-1 isolate with S15G E86Q E87Q C223H V321I mutations in complex with RNA template 5'-uagg, RNA primer 5'-pcc, MN2+, and udp
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
- 4WTM
- Type
- protein + RNA
- Length
- 558 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA template uagg; RNA primer cc; RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- Q99IB8
- Ligands
- UDP, MN, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | RNA template uagg | rna | 3 | — | — |
| P | RNA primer cc | rna | 2 | — | — |
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 553 | 48% helix, 16% strand | Q99IB8 |
Ligands and binding sites
- UDP · Uridine-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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.77 | 0.80 | 90 | MN, UDP |
| 2 | 231 | 0.72 | 0.88 | 36 | empty |
| 3 | 125 | 0.46 | 0.78 | 26 | empty |
| 4 | 64 | 0.39 | 0.79 | 17 | empty |
| 5 | 70 | 0.33 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- T–A · 577 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–A · 378 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–P · 105 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Compared structures
- 4WTM · 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 4WTM · PDBe 4WTM · UniProt Q99IB8
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