1M7D
Crystal structure of a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide complexed with a trisaccharide
- PDB DOI: https://doi.org/10.2210/pdb1M7D/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2002-07-19 Released: 2003-07-22 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.279 
- R-Value Work: 0.216 
wwPDB Validation   3D Report Full Report
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
light chain of the monoclonal antibody Fab SYA/J6 | 215 | Mus musculus | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for A2NHM3 (Mus musculus) Explore A2NHM3  Go to UniProtKB:  A2NHM3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A2NHM3 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
heavy chain of the monoclonal antibody Fab SYA/J6 | 220 | Mus musculus | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for P01801 (Mus musculus) Explore P01801  Go to UniProtKB:  P01801 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01801 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.279 
- R-Value Work: 0.216 
- Space Group: P 43 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 71 | α = 90 |
b = 71 | β = 90 |
c = 198 | γ = 90 |
Software Name | Purpose |
---|---|
Weissenberg | data collection |
WEIS | data reduction |
Protein | data reduction |
MERLOT | phasing |
CNS | refinement |
WEISSENBERG | data reduction |
WEIS | data scaling |
PROTEIN | data scaling |
Entry History 
Deposition Data
- Released Date: 2003-07-22  Deposition Author(s): Vyas, N.K., Vyas, M.N., Chervenak, M.C., Johnson, M.A., Pinto, B.M., Bundle, D.R., Quiocho, F.A.
Revision History (Full details and data files)
- Version 1.0: 2003-07-22
Type: Initial release - Version 1.1: 2008-04-28
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2011-11-16
Changes: Atomic model - Version 1.4: 2017-10-11
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary