2V90 | pdb_00002v90

Crystal structure of the 3rd PDZ domain of intestine- and kidney- enriched PDZ domain IKEPP (PDZD3)

• PDB DOI: https://doi.org/10.2210/pdb2V90/pdb

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


• Deposited: 2007-08-16 Released: 2007-08-28 
• Deposition Author(s): Uppenberg, J., Gileadi, C., Phillips, C., Elkins, J., Bunkoczi, G., Cooper, C., Pike, A.C.W., Salah, E., Ugochukwu, E., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Weigelt, J., Doyle, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the 3Rd Pdz Domain of Intestine- and Kidney-Enriched Pdz Domain Ikepp (Pdzd3)

Uppenberg, J., Gileadi, C., Phillips, C., Elkins, J., Bunkoczi, G., Cooper, C., Pike, A.C.W., Salah, E., Ugochukwu, E., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Weigelt, J., Doyle, D.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.83 kDa 
• Atom Count: 4,638 
• Modeled Residue Count: 566 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PDZ DOMAIN-CONTAINING PROTEIN 3	A, B, C, D, E, F	96	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q86UT5 (Homo sapiens) Explore Q86UT5  Go to UniProtKB:  Q86UT5
PHAROS:  Q86UT5 GTEx:  ENSG00000172367

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.15	α = 90
b = 97.95	β = 99.59
c = 59.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-28 
Deposition Author(s): Uppenberg, J., Gileadi, C., Phillips, C., Elkins, J., Bunkoczi, G., Cooper, C., Pike, A.C.W., Salah, E., Ugochukwu, E., Arrowsmith, C.H., Edwards, A., Sundstrom, M., Weigelt, J., Doyle, D.A.

Revision History  

• Version 1.0: 2007-08-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-02-28
  Changes: Source and taxonomy
• Version 1.3: 2020-03-04
  Changes: Derived calculations, Other
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Refinement description