8B82 | pdb_00008b82

Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide

• PDB DOI: https://doi.org/10.2210/pdb8B82/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, human papillomavirus 18
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-04 Released: 2023-10-18 
• Deposition Author(s): Stewart, B.Z., Kvansakul, M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.278 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide

Stewart, B.Z., Caria, S., Humbert, P.O., Kvansakul, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 27.42 kDa 
• Atom Count: 1,847 
• Modeled Residue Count: 233 
• Deposited Residue Count: 252 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein scribble homolog	A, B	116	Homo sapiens	Mutation(s): 0  Gene Names: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL
UniProt & NIH Common Fund Data Resources
Find proteins for Q14160 (Homo sapiens) Explore Q14160  Go to UniProtKB:  Q14160
PHAROS:  Q14160 GTEx:  ENSG00000180900

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein E6	C, D	10	human papillomavirus 18	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
CL	E [auth A], F [auth A], G [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.278 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.41	α = 90
b = 55.253	β = 90
c = 114.284	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Stewart, B.Z., Kvansakul, M.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1103871
Australian Research Council (ARC)	Australia	FT130101349

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary