7UAJ | pdb_00007uaj

Crystal structure of apo HPV16 E6

• PDB DOI: https://doi.org/10.2210/pdb7UAJ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia coli K-12, Human papillomavirus 16
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-13 Released: 2023-03-15 
• Deposition Author(s): Shen, Q., Leonard, P.G., Cross, J.B.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Starting Model: experimental

Literature

Disorder-to-order transition of the interdomain linker of HPV E6 upon E6AP binding reshapes p53 binding pocket

Shen, Q., Leonard, P.G., Cross, J.B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 245.54 kDa 
• Atom Count: 16,217 
• Modeled Residue Count: 2,041 
• Deposited Residue Count: 2,148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Protein E6	A, B, C, D	537	Escherichia coli K-12, Human papillomavirus 16 This entity is chimeric	Mutation(s): 0  Gene Names: malE, b4034, JW3994, E6
UniProt
Find proteins for P03126 (Human papillomavirus type 16) Explore P03126  Go to UniProtKB:  P03126
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
UniProt Groups	P03126P0AEX9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	E, F, G, H	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.11	α = 106.61
b = 88.68	β = 90.16
c = 109.61	γ = 102.76

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Shen, Q., Leonard, P.G., Cross, J.B.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary