2Z0U | pdb_00002z0u

Crystal structure of C2 domain of KIBRA protein

• PDB DOI: https://doi.org/10.2210/pdb2Z0U/pdb

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


• Deposited: 2007-05-07 Released: 2008-05-13 
• Deposition Author(s): Murayama, K., Kato-Murayama, M., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Crystal structure of C2 domain of KIBRA protein

Murayama, K., Kato-Murayama, M., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.19 kDa 
• Atom Count: 2,148 
• Modeled Residue Count: 256 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WW domain-containing protein 1	A, B	155	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IX03 (Homo sapiens) Explore Q8IX03  Go to UniProtKB:  Q8IX03
PHAROS:  Q8IX03 GTEx:  ENSG00000113645

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.456	α = 90
b = 88.928	β = 90
c = 36.698	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: 2008-05-13 
Deposition Author(s): Murayama, K., Kato-Murayama, M., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary