Research workbench
Crystal structure of hepatitis C virus ires junction iiiabc in complex with Fab HCV2
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
- 6U8D
- Type
- protein + RNA
- Length
- 508 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jiiiabc RNA (68-mer); Heavy chain of Fab HCV2; Light chain of Fab HCV2
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jiiiabc RNA (68-mer) | rna | 68 | — | — |
| H | Heavy chain of Fab HCV2 | protein | 225 | 8% helix, 52% strand | — |
| L | Light chain of Fab HCV2 | protein | 215 | 6% helix, 51% strand | — |
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 | 701 | 0.63 | 0.74 | 40 | empty |
| 2 | 249 | 0.55 | 0.77 | 36 | empty |
| 3 | 341 | 0.54 | 0.74 | 44 | empty |
| 4 | 253 | 0.43 | 0.72 | 22 | empty |
| 5 | 104 | 0.37 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2189 Ų buried · 26 hydrogen bonds · protein-protein
- A–H · 493 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–L · 200 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6U8D · Crystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV2 · 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 6U8D · PDBe 6U8D
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