5DQD
Structure of S55-5 Fab in complex with lipid A carbohydrate backbone
- PDB DOI: https://doi.org/10.2210/pdb5DQD/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Mutation(s): No 
- Deposited: 2015-09-14 Released: 2016-03-09 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.94 Å
- R-Value Free: 0.222 
- R-Value Work: 0.172 
- R-Value Observed: 0.175 
wwPDB Validation   3D Report Full Report
This is version 2.1 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 |
S55-5 Fab (IgG1 kappa) light chain | A [auth L] | 218 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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 |
S55-5 Fab (IgG1) heavy chain | B [auth H] | 222 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CL Query on CL | D [auth H], E [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.94 Å
- R-Value Free: 0.222 
- R-Value Work: 0.172 
- R-Value Observed: 0.175 
- Space Group: P 2 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 56.385 | α = 90 |
b = 64.793 | β = 90 |
c = 129.771 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
Entry History 
Deposition Data
- Released Date: 2016-03-09  Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.
Revision History (Full details and data files)
- Version 1.0: 2016-03-09
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary