8HDG | pdb_00008hdg

Small peptide enhances the binding of nutline-3a to MdmX

PDB DOI: https://doi.org/10.2210/pdb8HDG/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia
Mutation(s): No

Deposited: 2022-11-04 Released: 2022-11-30
Deposition Author(s): Cheng, X.Y., Huang, Y., Wei, Q.Y., Huang, J.J., Peng, Y.W., Su, Z.D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.241 (Depositor), 0.241 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Small peptide enhances the binding of nutline-3a to MdmX

Cheng, X.Y., Huang, Y., Wei, Q.Y., Huang, J.J., Peng, Y.W., Su, Z.D.

To be published.

Macromolecule Content

Total Structure Weight: 54.32 kDa
Atom Count: 3,483
Modeled Residue Count: 392
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein DKFZp686B01123	A [auth D], B [auth A], C, D [auth B]	111	Homo sapiens	Mutation(s): 0 Gene Names: DKFZp686B01123
UniProt & NIH Common Fund Data Resources
Find proteins for O15151 (Homo sapiens) Explore O15151 Go to UniProtKB: O15151
PHAROS: O15151 GTEx: ENSG00000198625
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15151
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NUT (Subject of Investigation/LOI) Query on NUT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain I [auth C] SDF format, chain E [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth C] MOL2 format, chain E [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth C] mmCIF format, chain E [auth D]	E [auth D], G [auth A], I [auth C], J [auth B]	4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one C₃₀ H₃₀ Cl₂ N₄ O₄ BDUHCSBCVGXTJM-WUFINQPMSA-N		Interactions Focus chain E [auth D] Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth B] Interactions & Density Focus chain E [auth D] Focus chain G [auth A] Focus chain I [auth C] Focus chain J [auth B]
O4B Query on O4B Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	F [auth D], H [auth A], K [auth B], L [auth B]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C₁₂ H₂₄ O₆ XEZNGIUYQVAUSS-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth D] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
NUT	BindingDB: 8HDG	Ki: min: 1599, max: 6.90e+4 (nM) from 2 assay(s)
		Kd: 6500 (nM) from 1 assay(s)
		IC50: 4300 (nM) from 1 assay(s)