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'-uacc, RNA primer 5'-pgg, 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
- 4WTL
- Type
- protein + RNA
- Length
- 558 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA template uacc; RNA primer gg; RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- Q99IB8
- Ligands
- UDP, MN, CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | RNA template uacc | rna | 3 | — | — |
| P | RNA primer gg | rna | 2 | — | — |
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 553 | 49% helix, 16% strand | Q99IB8 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains T, P, A
- MN · Manganese (II) ion · metal · 2 copies · chains P, A
- CL · Chloride ion · ion · chains A
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains A
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.74 | 0.78 | 68 | empty |
| 2 | 75 | 0.72 | 0.97 | 23 | empty |
| 3 | 580 | 0.68 | 0.78 | 58 | MN, UDP |
| 4 | 60 | 0.42 | 0.81 | 17 | empty |
| 5 | 124 | 0.41 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- T–A · 540 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–A · 401 Ų buried · 7 hydrogen bonds · protein-nucleic
- T–P · 110 Ų buried · 8 hydrogen bonds · nucleic-nucleic
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 4WTL · PDBe 4WTL · UniProt Q99IB8
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