MolNFT v1 · #14380 · protein
Crystal structure of a monoclonal Fab specific for shigella flexneri Y lipopolysaccharide complexed with a trisaccharide
1M7D · Light chain of the monoclonal antibody Fab SYA/J6: “Crystal structure of a monoclonal Fab specific for shigella flexneri Y lipopolysaccharide complexed with a…”. X-ray diffraction, 3 ligands (RAE, MAG, RAM), 6 pockets (best…
- PDB
- 1M7D
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of the monoclonal antibody Fab SYA/J6; Heavy chain of the monoclonal antibody…
- Ligands
- RAE, MAG, RAM
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light chain of the monoclonal antibody Fab SYA/J6 | protein | 215 | 7% helix, 53% strand | — |
| B | Heavy chain of the monoclonal antibody Fab SYA/J6 | protein | 220 | 7% helix, 51% strand | — |
Ligands and binding sites
- RAE · alpha-L-Olivopyranose · ligand · chains A, B
- MAG · methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside · sugar · chains A, B
- RAM · alpha-L-rhamnopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.62 | 0.74 | 66 | empty |
| 2 | 118 | 0.53 | 0.82 | 28 | empty |
| 3 | 84 | 0.52 | 0.84 | 18 | empty |
| 4 | 140 | 0.46 | 0.77 | 23 | MAG, RAE, RAM |
| 5 | 113 | 0.42 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1752 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1M7D · Crystal structure of a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide… · 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 1M7D · PDBe 1M7D
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