2DYQ | pdb_00002dyq

Crystal Structure of the C-terminal Phophotyrosine Interaction Domain of Human APBB3

• PDB DOI: https://doi.org/10.2210/pdb2DYQ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2006-09-16 Released: 2007-09-18 
• Deposition Author(s): Nishino, A., Saijo, S., Kishishita, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.298 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Literature

Crystal Structure of the C-terminal Phophotyrosine Interaction Domain of Human APBB3

Saijo, S., Nishino, A., Kishishita, S., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.58 kDa 
• Atom Count: 909 
• Modeled Residue Count: 124 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 precursor protein-binding family B member 3	A	144	Homo sapiens	Mutation(s): 0  Gene Names: APBB3, FE65L2
UniProt & NIH Common Fund Data Resources
Find proteins for O95704 (Homo sapiens) Explore O95704  Go to UniProtKB:  O95704
GTEx:  ENSG00000113108

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: 3.10 Å
• R-Value Free:  0.298 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.292	α = 90
b = 82.292	β = 90
c = 104.871	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-18 
Deposition Author(s): Nishino, A., Saijo, S., Kishishita, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-09-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary