4ODV
Fab Structure of lipid A-specific antibody A6 in complex with lipid A carbohydrate backbone
- PDB DOI: https://doi.org/10.2210/pdb4ODV/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Mutation(s): No 
- Deposited: 2014-01-10 Released: 2015-06-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.249 
- R-Value Work: 0.204 
- R-Value Observed: 0.207 
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 |
A6 Fab (IgG2b kappa) light chain | A [auth L] | 215 | 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 |
A6 Fab (IgG2b) 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 | |
PEG Query on PEG | D [auth H] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.249 
- R-Value Work: 0.204 
- R-Value Observed: 0.207 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 37.563 | α = 90 |
b = 64.285 | β = 90 |
c = 154.157 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Macromolecular | data collection |
HKL-2000 | data reduction |
Entry History 
Deposition Data
- Released Date: 2015-06-24  Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.
Revision History (Full details and data files)
- Version 1.0: 2015-06-24
Type: Initial release - Version 1.1: 2015-07-01
Changes: Database references - Version 1.2: 2015-10-07
Changes: Database references - Version 1.3: 2017-11-22
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary