3OKO
Crystal structure of S25-39 in complex with Kdo(2.8)Kdo(2.4)Kdo
- PDB DOI: https://doi.org/10.2210/pdb3OKO/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Mutation(s): No 
- Deposited: 2010-08-25 Released: 2011-04-06 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.267 
- R-Value Work: 0.210 
- R-Value Observed: 0.213 
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 |
S25-39 Fab (IgG1k) light chain | A [auth B] | 222 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
S25-39 Fab (IgG1k) heavy chain | B [auth A] | 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 | 3 | N/A | N/A | |
Glycosylation Resources | |||||
GlyTouCan:  G25386BJ GlyCosmos:  G25386BJ |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
ZN Query on ZN | D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.267 
- R-Value Work: 0.210 
- R-Value Observed: 0.213 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 45.441 | α = 90 |
b = 81.394 | β = 90 |
c = 129.009 | γ = 90 |
Software Name | Purpose |
---|---|
d*TREK | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
Entry History 
Deposition Data
- Released Date: 2011-04-06  Deposition Author(s): Blackler, R.J., Evans, S.V.
Revision History (Full details and data files)
- Version 1.0: 2011-04-06
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2018-03-07
Changes: Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary