2OCS | pdb_00002ocs

The crystal structure of the first PDZ domain of human NHERF-2 (SLC9A3R2)

• PDB DOI: https://doi.org/10.2210/pdb2OCS/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-12-21 Released: 2007-01-16 
• Deposition Author(s): Papagrigoriou, E., Phillips, C., Gileadi, C., Elkins, J., Salah, E., Berridge, G., Savitsky, P., Gorrec, F., Umeano, C., Ugochukwu, E., Gileadi, O., Burgess, N., Edwards, A., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Doyle, D.A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.198 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: in silico

Literature

The crystal structure of the first PDZ domain of human NHERF-2 (SLC9A3R2)

Papagrigoriou, E., Phillips, C., Gileadi, C., Elkins, J., Salah, E., Berridge, G., Savitsky, P., Gorrec, F., Umeano, C., Ugochukwu, E., Gileadi, O., Burgess, N., Edwards, A., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Doyle, D.A.

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: 9.91 kDa 
• Atom Count: 762 
• Modeled Residue Count: 85 
• Deposited Residue Count: 88 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)/H(+) exchange regulatory cofactor NHE-RF2	A	88	Homo sapiens	Mutation(s): 0  Gene Names: SLC9A3R2, NHERF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15599 (Homo sapiens) Explore Q15599  Go to UniProtKB:  Q15599
PHAROS:  Q15599 GTEx:  ENSG00000065054

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN	B [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.198 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.556	α = 90
b = 39.867	β = 106.93
c = 37.278	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-16 
Deposition Author(s): Papagrigoriou, E., Phillips, C., Gileadi, C., Elkins, J., Salah, E., Berridge, G., Savitsky, P., Gorrec, F., Umeano, C., Ugochukwu, E., Gileadi, O., Burgess, N., Edwards, A., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Doyle, D.A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-01-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description