8B9T | pdb_00008b9t

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

• PDB DOI: https://doi.org/10.2210/pdb8B9T/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Human papillomavirus 16
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-07 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: 2.50 Å
• R-Value Free: 
  0.281 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.274 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.275 (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: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 12.36 kDa 
• Atom Count: 828 
• Modeled Residue Count: 98 
• Deposited Residue Count: 106 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein scribble homolog	A	96	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	B	10	Human papillomavirus 16	Mutation(s): 0
UniProt
Find proteins for P03126 (Human papillomavirus type 16) Explore P03126  Go to UniProtKB:  P03126

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A], E [auth A], F [auth A], G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
IPA	H [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.281 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.274 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.275 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.611	α = 90
b = 70.611	β = 90
c = 140.782	γ = 120

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