MolNFT v1 · #157369 · protein + RNA
Crystal structure of hepatitis a virus ires domain V in complex with Fab havx
6MWN · Hav dv RNA (92-mer): “Crystal structure of hepatitis a virus ires domain V in complex with Fab havx”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #157369 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6MWN
- Type
- protein + RNA
- Length
- 1,060 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hav dv RNA (92-mer); Fab havx heavy chain; Fab havx light chain
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hav dv RNA (92-mer) | rna | 92 | — | — |
| C, H | Fab havx heavy chain | protein | 225 | 7% helix, 49% strand | — |
| D, L | Fab havx light chain | protein | 213 | 5% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.75 | 0.84 | 45 | empty |
| 2 | 310 | 0.70 | 0.84 | 25 | empty |
| 3 | 540 | 0.62 | 0.76 | 30 | empty |
| 4 | 611 | 0.62 | 0.75 | 28 | empty |
| 5 | 541 | 0.59 | 0.74 | 28 | empty |
Interfaces
11 interfaces between chains.
- H–L · 1937 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1937 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 894 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 889 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–L · 497 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nucleotide modification).
Compared structures
- 6MWN · Crystal structure of hepatitis A virus IRES domain V in complex with Fab HAVx · 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 6MWN · PDBe 6MWN
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