7EDS

Human p53 core domain with germline hot spot mutation M133T in complex with the natural PIG3 p53-response element and Arsenic

• PDB DOI: https://doi.org/10.2210/pdb7EDS/pdb
• NAKB: 7EDS

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-03-17 Released: 2022-06-22 
• Deposition Author(s): Xing, Y.F., Lu, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.227 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Arsenic-bound p53 Hotspot mutant M133T in complex with the natural PIG3 p53-response element

Xing, Y.F., Lu, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.07 kDa 
• Atom Count: 2,830 
• Modelled Residue Count: 253 
• Deposited Residue Count: 260 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	A	200	Homo sapiens	Mutation(s): 1  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: 2
Molecule	Chains	Length	Organism	Image
PIG3 sense strand	B [auth R]	30	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
PIG3 anti-sense strand	C [auth F]	30	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARS (Subject of Investigation/LOI)	D [auth A]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.227 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.53	α = 90
b = 49.88	β = 93.31
c = 33.95	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Xing, Y.F., Lu, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81861130368

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description