MolNFT v1 · #28709 · protein
Anti-HCV Fab 19D9D6 complexed with protein L (ppl) mutant A66W
1YMH · Fab 16D9D6, light chain: “Anti-HCV Fab 19D9D6 complexed with protein L (ppl) mutant A66W”. X-ray diffraction, 16 pockets (best druggability 0.65). MolNFT v1 #28709 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YMH
- Type
- protein
- Length
- 1,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 16D9D6, light chain; Fab 16D9D6, heavy chain; Protein L
- UniProt
- Q51918
- Pockets
- 16 · best druggability 0.65
Structure
x-ray diffraction · 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.