7EEU | pdb_00007eeu

Human p53 core domain with hot spot mutation R282W in complex with the natural CDKN1A(p21) p53-response element and Arsenic

PDB DOI: https://doi.org/10.2210/pdb7EEU/pdb
NAKB: 7EEU

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

Deposited: 2021-03-19 Released: 2022-06-22
Deposition Author(s): Xing, Y.F., Lu, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.264 (Depositor), 0.253 (DCC)
R-Value Work:
0.234 (Depositor), 0.225 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Human p53 core domain with hot spot mutation R282W in complex with the natural CDKN1A(p21) p53-response element and Arsenic

Xing, Y.F., Lu, M.

To be published.

Macromolecule Content

Total Structure Weight: 218.51 kDa
Atom Count: 14,988
Modeled Residue Count: 1,703
Deposited Residue Count: 1,720
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	A, B, C, D, E A, B, C, D, E, F, G, H	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04637
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
CDKN1A(p21) sense strand	I, K	30	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
CDKN1A(p21) anti-sense strand	J, L	30	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain W [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E]	W [auth E], Z [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain W [auth E] Focus chain Z [auth F]
ARS (Subject of Investigation/LOI) Query on ARS Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain CA [auth H] SDF format, chain AA [auth G] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain CA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain CA [auth H] mmCIF format, chain AA [auth G]	AA [auth G] CA [auth H] M [auth A] O [auth B] Q [auth C] AA [auth G], CA [auth H], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], X [auth F]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth H] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain X [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain V [auth E] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain DA [auth H] SDF format, chain BA [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain DA [auth H] MOL2 format, chain BA [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain DA [auth H] mmCIF format, chain BA [auth G]	BA [auth G] DA [auth H] N [auth A] P [auth B] R [auth C] BA [auth G], DA [auth H], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], Y [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain DA [auth H] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth H] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain Y [auth F]