Research workbench
The solution structure of a trisaccharide-antibody complex: comparison of NMR measurements with a crystal structure
Analyse The solution structure of a trisaccharide-antibody complex: comparison of NMR… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MFD
- Type
- protein
- Length
- 423 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-lambda SE155-4 Fab (light chain); IGG1-lambda SE155-4 Fab (heavy chain)
- Ligands
- ABE, MMA, GLA
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-lambda SE155-4 Fab (light chain) | protein | 212 | 7% helix, 56% strand | — |
| H | IGG1-lambda SE155-4 Fab (heavy chain) | protein | 211 | 10% helix, 54% strand | — |
Ligands and binding sites
- ABE · alpha-D-Abequopyranose · ligand · chains L, H
- MMA · methyl alpha-D-mannopyranoside · sugar · chains H
- GLA · alpha-D-galactopyranose · sugar · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.66 | 0.76 | 59 | empty |
| 2 | 54 | 0.39 | 0.80 | 14 | ABE |
Interfaces
1 interface between chains.
- L–H · 1836 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1MFD · The solution structure of a trisaccharide-antibody complex: comparison of NMR… · the same entry in another collection · chain L against L, 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 1MFD · PDBe 1MFD
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