Research workbench
Structure of DC8E8 Fab crystallized at pH 8.5
Analyse Structure of DC8E8 Fab crystallized at pH 8.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MX3
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.98
- Source
- Mus musculus
- Molecule
- antibody Fab heavy chain; antibody kappa chain
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.98 · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | antibody Fab heavy chain | protein | 220 | 8% helix, 50% strand | — |
| L, B | antibody kappa chain | protein | 218 | 5% helix, 54% strand | — |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.72 | 0.76 | 105 | empty |
| 2 | 751 | 0.67 | 0.75 | 64 | empty |
| 3 | 755 | 0.67 | 0.75 | 66 | empty |
| 4 | 187 | 0.54 | 0.79 | 28 | empty |
| 5 | 171 | 0.51 | 0.78 | 29 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1865 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1839 Ų buried · 18 hydrogen bonds · protein-protein
- H–A · 272 Ų buried · 9 hydrogen bonds · protein-protein
- H–B · 98 Ų buried · 0 hydrogen bonds · protein-protein
- L–A · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5MX3 · Structure of DC8E8 Fab crystallized at pH 8.5 · 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 5MX3 · PDBe 5MX3
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