7JZR | pdb_00007jzr

CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALAEB

• PDB DOI: https://doi.org/10.2210/pdb7JZR/pdb

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


• Deposited: 2020-09-02 Released: 2021-10-06 
• Deposition Author(s): Gill, N.P., Madden, D.R.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALAEB

Gill, N.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 21.21 kDa 
• Atom Count: 1,647 
• Modeled Residue Count: 188 
• Deposited Residue Count: 194 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Golgi-associated PDZ and coiled-coil motif-containing protein	A, B	87	Homo sapiens	Mutation(s): 0  Gene Names: GOPC, CAL, FIG
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD26 (Homo sapiens) Explore Q9HD26  Go to UniProtKB:  Q9HD26
PHAROS:  Q9HD26 GTEx:  ENSG00000047932

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LyCALAEB peptide core	C, D	10	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VU4 (Subject of Investigation/LOI)	E [auth C], F [auth D]	4-(2-aminoethyl)benzoic acid C9 H11 N O2 MRBFWTDIRYEDBQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.362	α = 90
b = 47.468	β = 90
c = 98.024	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
PHENIX	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Gill, N.P., Madden, D.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01-DK101541
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20-GM113132
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	P30-DK117469
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM008704

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 2.0: 2022-02-02
  Type: Coordinate replacement
  Reason: Polymer geometry
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.2: 2024-11-13
  Changes: Structure summary