2YYO

Crystal structure of human SPRY domain

• PDB DOI: https://doi.org/10.2210/pdb2YYO/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-04-30 Released: 2008-05-06 
• Deposition Author(s): Kishishita, S., Uchikubo-Kamo, T., Murayama, K., Terada, T., Chen, L., Fu, Z.Q., Chrzas, J., Shirouzu, M., Wang, B.C., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Crystal structure of human SPRY domain

Kishishita, S., Uchikubo-Kamo, T., Murayama, K., Terada, T., Chen, L., Fu, Z.Q., Chrzas, J., Shirouzu, M., Wang, B.C., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.26 kDa 
• Atom Count: 1,305 
• Modelled Residue Count: 160 
• Deposited Residue Count: 171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPRY domain-containing protein 3	A	171	Homo sapiens	Mutation(s): 0  Gene Names: SPRYD3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NCJ5 (Homo sapiens) Explore Q8NCJ5  Go to UniProtKB:  Q8NCJ5
PHAROS:  Q8NCJ5 GTEx:  ENSG00000167778

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.107	α = 90
b = 52.107	β = 90
c = 108.583	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Kishishita, S., Uchikubo-Kamo, T., Murayama, K., Terada, T., Chen, L., Fu, Z.Q., Chrzas, J., Shirouzu, M., Wang, B.C., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-09-09
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary