3GGE | pdb_00003gge

Crystal structure of the PDZ domain of PDZ domain-containing protein GIPC2

• PDB DOI: https://doi.org/10.2210/pdb3GGE/pdb

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


• Deposited: 2009-02-27 Released: 2009-03-24 
• Deposition Author(s): Chaikuad, A., Hozjan, V., Yue, W., Cooper, C., Elkins, J., Pike, A.C.W., Roos, A.K., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the PDZ domain of PDZ domain-containing protein GIPC2

Chaikuad, A., Hozjan, V., Yue, W., Cooper, C., Elkins, J., Pike, A.C.W., Roos, A.K., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Oppermann, U.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.18 kDa 
• Atom Count: 2,322 
• Modeled Residue Count: 282 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PDZ domain-containing protein GIPC2	A, B, C	95	Homo sapiens	Mutation(s): 0  Gene Names: GIPC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF65 (Homo sapiens) Explore Q8TF65  Go to UniProtKB:  Q8TF65
PHAROS:  Q8TF65 GTEx:  ENSG00000137960

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth B], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.51	α = 90
b = 83.51	β = 90
c = 160.31	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Chaikuad, A., Hozjan, V., Yue, W., Cooper, C., Elkins, J., Pike, A.C.W., Roos, A.K., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description