6V84 | pdb_00006v84

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

• PDB DOI: https://doi.org/10.2210/pdb6V84/pdb

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


• Deposited: 2019-12-10 Released: 2021-02-03 
• 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: 1.64 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

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

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: 21.43 kDa 
• Atom Count: 1,710 
• 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, C [auth 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
LyCALAc	B [auth C], D	10	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B [auth C], D	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.568	α = 90
b = 47.741	β = 90
c = 97.448	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-03 
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: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Author supporting evidence, Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary