4XR8

Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4XR8/pdb

• Classification: VIRAL PROTEIN/ ANTITUMOR PROTEIN
• Organism(s): Escherichia coli K-12, Homo sapiens, Human papillomavirus 16
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2015-01-20 Released: 2016-02-03 
• Deposition Author(s): Martinez-Zapien, D., Ruiz, F.X., Mitschler, A., Podjarny, A., Trave, G., Zanier, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.246 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 166.67 kDa 
• Atom Count: 12,034 
• Modelled Residue Count: 1,456 
• Deposited Residue Count: 1,466 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein, ubiquitin ligase E6AP	A, B	383	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 6  Gene Names: malE, b4034, JW3994
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q05086 (Homo sapiens) Explore Q05086  Go to UniProtKB:  Q05086
PHAROS:  Q05086 GTEx:  ENSG00000114062
UniProt Groups	Q05086P0AEX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	C, D	199	Homo sapiens	Mutation(s): 0  Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
PHAROS:  P04637 GTEx:  ENSG00000141510

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein E6	E [auth F], F [auth H]	151	Human papillomavirus 16	Mutation(s): 4  Gene Names: E6
UniProt
Find proteins for P03126 (Human papillomavirus type 16) Explore P03126  Go to UniProtKB:  P03126

Oligosaccharides

Help

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	I [auth A], J [auth B], M [auth D], Q [auth F]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	K [auth C], L [auth D], N [auth F], O [auth F], R [auth H], S [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	P [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	G [auth E], H [auth G]	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.246 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.842	α = 90
b = 128.939	β = 92.33
c = 81.56	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Martinez-Zapien, D., Ruiz, F.X., Mitschler, A., Podjarny, A., Trave, G., Zanier, K.

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary