1IKO
CRYSTAL STRUCTURE OF THE MURINE EPHRIN-B2 ECTODOMAIN
- PDB DOI: https://doi.org/10.2210/pdb1IKO/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Mus musculus
- Expression System: Komagataella pastoris
- Mutation(s): No 
- Deposited: 2001-05-03 Released: 2002-05-03 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.92 Å
- R-Value Free: 0.249 
- R-Value Work: 0.216 
- R-Value Observed: 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 |
EPHRIN-B2 | A [auth P] | 178 | Mus musculus | Mutation(s): 0  Gene Names: ephrin-B2 | |
UniProt | |||||
Find proteins for P52800 (Mus musculus) Explore P52800  Go to UniProtKB:  P52800 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P52800 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B [auth A] | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.92 Å
- R-Value Free: 0.249 
- R-Value Work: 0.216 
- R-Value Observed: 0.216 
- Space Group: P 65 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 59.283 | α = 90 |
b = 59.283 | β = 90 |
c = 168.868 | γ = 120 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
HKL-2000 | data reduction |
SHARP | phasing |
CNS | refinement |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2002-05-03  Deposition Author(s): Toth, J., Cutforth, T., Gelinas, A.D., Bethoney, K.A., Bard, J., Harrison, C.J.
Revision History (Full details and data files)
- Version 1.0: 2002-05-03
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary