Research workbench
Crystal structure of hepatitis C virus ires junction iiiabc in complex with Fab HCV3
Analyse Crystal structure of hepatitis C virus ires junction iiiabc in complex with Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U8K
- Type
- protein + RNA
- Length
- 1,515 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jiiiabc RNA (68-mer); Heavy chain of Fab HCV3; Light chain of Fab HCV3
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Jiiiabc RNA (68-mer) | rna | 68 | — | — |
| D, F, H | Heavy chain of Fab HCV3 | protein | 222 | 9% helix, 50% strand | — |
| E, G, L | Light chain of Fab HCV3 | protein | 215 | 6% helix, 52% strand | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.72 | 0.77 | 48 | empty |
| 2 | 740 | 0.69 | 0.77 | 39 | empty |
| 3 | 619 | 0.68 | 0.78 | 31 | empty |
| 4 | 637 | 0.67 | 0.76 | 88 | empty |
| 5 | 521 | 0.60 | 0.74 | 66 | empty |
Interfaces
13 interfaces between chains.
- H–L · 2001 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1968 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 1949 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 899 Ų buried · 25 hydrogen bonds · protein-nucleic
- E–L · 891 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6U8K · Crystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV3 · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6U8K · PDBe 6U8K
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