5JK9
Crystal structure of human IZUMO1
- PDB DOI: https://doi.org/10.2210/pdb5JK9/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Drosophila
- Mutation(s): No 
- Deposited: 2016-04-26 Released: 2016-06-22 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.231 
- R-Value Work: 0.194 
- R-Value Observed: 0.196 
This is version 1.3 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 |
Izumo sperm-egg fusion protein 1 | 246 | Homo sapiens | Mutation(s): 0  Gene Names: IZUMO1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q8IYV9 (Homo sapiens) Explore Q8IYV9  Go to UniProtKB:  Q8IYV9 | |||||
PHAROS:  Q8IYV9 GTEx:  ENSG00000182264  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q8IYV9 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.231 
- R-Value Work: 0.194 
- R-Value Observed: 0.196 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 64.936 | α = 77.65 |
b = 75.067 | β = 79.11 |
c = 108.885 | γ = 70.66 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
autoSHARP | phasing |
Entry History 
Deposition Data
- Released Date: 2016-06-22  Deposition Author(s): Ohto, U., Ishida, H., Shimizu, T.
Revision History (Full details and data files)
- Version 1.0: 2016-06-22
Type: Initial release - Version 1.1: 2016-06-29
Changes: Database references - Version 1.2: 2020-02-19
Changes: Data collection, Database references, Derived calculations - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary