8XCB | pdb_00008xcb

Cocrystal structure of p53 in complex of B20

PDB DOI: https://doi.org/10.2210/pdb8XCB/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.245 (Depositor), 0.250 (DCC)
R-Value Work:
0.215 (Depositor), 0.221 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Cocrystal structure of p53 in complex of B20

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

To be published.

Macromolecule Content

Total Structure Weight: 90.91 kDa
Atom Count: 6,672
Modeled Residue Count: 773
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04637
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LUZ Query on A1LUZ Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D]	G [auth B], K [auth D]	2-[2,4-bis(oxidanylidene)-1,3-thiazolidin-5-ylidene]ethanoic acid C₅ H₃ N O₄ S GZMAUGAAAMRIDY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain K [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D]	F [auth A], J [auth C], M [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth C] Focus chain M [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D]	E [auth A], H [auth B], I [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.245 (Depositor), 0.250 (DCC)
R-Value Work: 0.215 (Depositor), 0.221 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.853	α = 90
b = 69.782	β = 89.97
c = 83.669	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

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		Shanghai Youth Talent Development Program (2017275)
Other government		Foundation of National Facility for Translational Medicine (Shanghai) (TMSK-2020-003)
Other government		Foundation of National Facility for Translational Medicine (Shanghai) (TMSK-2020-003)
Other government		Shanghai Medical and Health Excellent Discipline Leader Development Plan (2018BR36)