4M7J
Crystal structure of S25-26 in complex with Kdo(2.8)Kdo(2.4)Kdo trisaccharide
- PDB DOI: https://doi.org/10.2210/pdb4M7J/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Mutation(s): No 
- Deposited: 2013-08-12 Released: 2014-04-09 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.247 
- R-Value Work: 0.212 
- R-Value Observed: 0.213 
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 |
S25-26 Fab (IgG1k) heavy chain | A [auth H] | 219 | 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 |
S25-26 Fab (Igg1k) light chain | B [auth L] | 219 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid | C [auth A] | 3 | N/A | N/A | |
Glycosylation Resources | |||||
GlyTouCan:  G25386BJ GlyCosmos:  G25386BJ |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | D [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PEG Query on PEG | F [auth L] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
K Query on K | E [auth H] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.247 
- R-Value Work: 0.212 
- R-Value Observed: 0.213 
- Space Group: P 32 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 74.464 | α = 90 |
b = 74.464 | β = 90 |
c = 149.893 | γ = 120 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Macromolecular | data collection |
Entry History 
Deposition Data
- Released Date: 2014-04-09  Deposition Author(s): Haji-Ghassemi, O., Evans, S.V., Muller-Loennies, S., Saldova, R., Muniyappa, M., Brade, L., Rudd, P.M., Harvey, D.J., Kosma, P., Brade, H.
Revision History (Full details and data files)
- Version 1.0: 2014-04-09
Type: Initial release - Version 1.1: 2014-06-11
Changes: Database references - Version 1.2: 2014-07-09
Changes: Database references - Version 1.3: 2017-11-15
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, Refinement description, Structure summary