Research workbench
Crystal Structure Anti-Oxycodone Antibody HY2-A12 Fab Complexed with Oxycodone
Analyse Crystal Structure Anti-Oxycodone Antibody HY2-A12 Fab Complexed with Oxycodone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U63
- Type
- protein
- Length
- 1,258 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Mus musculus
- Molecule
- HY2-A12 Fab Light Chain; HY2-A12 Fab Heavy Chain
- Ligands
- OOX
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.3 · 3 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A, C | HY2-A12 Fab Light Chain | protein | 209 | 8% helix, 55% strand | — |
| H | HY2-A12 Fab Heavy Chain | protein | 201 | 6% helix, 53% strand | — |
| B, D | HY2-A12 Fab Heavy Chain | protein | 215 | 6% helix, 51% strand | — |
Ligands and binding sites
- OOX · 14-hydroxy-3-methoxy-17-methyl-5beta-4,5-epoxymorphinan-6-one · ligand · 3 copies · chains L, H, A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.73 | 0.76 | 94 | empty |
| 2 | 541 | 0.65 | 0.77 | 71 | empty |
| 3 | 593 | 0.64 | 0.75 | 53 | empty |
| 4 | 361 | 0.55 | 0.74 | 38 | empty |
| 5 | 177 | 0.45 | 0.75 | 22 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1839 Ų buried · 14 hydrogen bonds · protein-protein
- L–H · 1813 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1799 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 356 Ų buried · 8 hydrogen bonds · protein-protein
- H–C · 268 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7U63 · PDBe 7U63
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