Research workbench
anti-HCV Fab 19D9D6 complexed with protein L (PpL) mutant A66W
Analyse anti-HCV Fab 19D9D6 complexed with protein L (PpL) mutant A66W in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YMH
- Type
- protein
- Length
- 1,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Finegoldia magna; Mus musculus
- Molecule
- Fab 16D9D6, light chain; Fab 16D9D6, heavy chain; Protein L
- UniProt
- Q51918
- Pockets
- 16 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.6 · 3 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fab 16D9D6, light chain | protein | 220 | 5% helix, 44% strand | — |
| B, D | Fab 16D9D6, heavy chain | protein | 218 | 10% helix, 49% strand | — |
| E, F | Protein L | protein | 65 | 29% helix, 40% strand | Q51918 |
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.65 | 0.74 | 86 | empty |
| 2 | 291 | 0.62 | 0.80 | 55 | empty |
| 3 | 491 | 0.60 | 0.74 | 73 | empty |
| 4 | 215 | 0.58 | 0.80 | 35 | empty |
| 5 | 134 | 0.55 | 0.82 | 24 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1986 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1896 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 735 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 626 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 598 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1YMH · Anti-HCV Fab 19D9D6 complexed with protein L (ppl) mutant A66W · 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
- Every structure of UniProt Q51918
- Elsewhere: RCSB PDB 1YMH · PDBe 1YMH · UniProt Q51918
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