5IC3 | pdb_00005ic3

CAL PDZ domain with peptide and inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5IC3/pdb

• Classification: PEPTIDE BINDING PROTEIN/INHIBITOR
• Organism(s): Homo sapiens, Alphapapillomavirus 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-22 Released: 2017-08-09 
• Deposition Author(s): Zhao, Y., Madden, D.R.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

CAL PDZ domain with peptide and inhibitor

Zhao, Y., Madden, D.R.

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: 21.57 kDa 
• Atom Count: 1,609 
• Modeled Residue Count: 184 
• 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
HPV18E6 Peptide	C, D	10	Alphapapillomavirus 7	Mutation(s): 0
UniProt
Find proteins for P06463 (Human papillomavirus type 18) Explore P06463  Go to UniProtKB:  P06463

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PQR	E [auth A]	4-[methyl(nitroso)amino]benzene-1,2-diol C7 H8 N2 O3 XAKAQCMEMMZUEO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.772	α = 90
b = 48.252	β = 101.47
c = 51.639	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PHENIX	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Zhao, Y., 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

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary