8XCE | pdb_00008xce

cocrystal structure of p53 in complex of B23

• PDB DOI: https://doi.org/10.2210/pdb8XCE/pdb

• Classification: ANTITUMOR PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-12-08 Released: 2025-06-11 
• Deposition Author(s): Wang, Z., Shujun, X., Yigang, T., Derun, Z., Jiaqi, W., Kai, K., Lu, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.223 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

cocrystal structure of p53 in complex of B23

Wang, Z., Taijie, G., Shujun, X., Huaxin, S., Yigang, T., Xueqin, C., Fangfang, S., Kai, K., Lirong, Z., Derun, Z., Jiaqi, W., Jingyi, C., Hesong, Z., Lu, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 90.56 kDa 
• Atom Count: 6,437 
• Modeled Residue Count: 770 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	A, B, C, D	200	Homo sapiens	Mutation(s): 0  Gene Names: TP53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
PHAROS:  P04637 GTEx:  ENSG00000141510

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LU0	I [auth D]	2-[(2~{Z})-2-(3-ethynylphenyl)imino-4-oxidanylidene-1,3-thiazolidin-5-ylidene]ethanoic acid C13 H8 N2 O3 S GQXBNBYNTFWKFU-UHFFFAOYSA-N
ZN	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.223 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.93	α = 90
b = 71.8	β = 90
c = 84.62	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Wang, Z., Shujun, X., Yigang, T., Derun, Z., Jiaqi, W., Kai, K., Lu, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81622002
National Natural Science Foundation of China (NSFC)	China	81861130368
Other government	China	Shanghai Youth Talent Development Program (2017275)
Other government	China	Shanghai Collaborative Innovation Center for Translational Medicine (TM201902)
Other government	China	Foundation of National Facility for Translational Medicine (Shanghai) (TMSK-2020-003)
Other government	China	Shanghai Medical and Health Excellent Discipline Leader Development Plan (2018BR36)

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release