8IA5 | pdb_00008ia5

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

• PDB DOI: https://doi.org/10.2210/pdb8IA5/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-07 Released: 2023-02-22 
• Deposition Author(s): Cheng, X.Y., Wei, Q.Y., Huang, Y., Su, Z.D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.284 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

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

Cheng, X.Y., Wei, Q.Y., Huang, Y., Su, Z.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 12.19 kDa 
• Atom Count: 890 
• Modeled Residue Count: 95 
• Deposited Residue Count: 99 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Mdm4	A	90	Homo sapiens	Mutation(s): 0  Gene Names: MDM4, MDMX
UniProt & NIH Common Fund Data Resources
Find proteins for O15151 (Homo sapiens) Explore O15151  Go to UniProtKB:  O15151
PHAROS:  O15151 GTEx:  ENSG00000198625

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
9-mer peptide	B	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NUT (Subject of Investigation/LOI)	C [auth A]	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
O4B	D [auth A]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C12 H24 O6 XEZNGIUYQVAUSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NUT	BindingDB:  8IA5	Ki: min: 1599, max: 6.90e+4 (nM) from 2 assay(s)
		IC50: min: 4300, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.284 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.220 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.08	α = 90
b = 47.08	β = 90
c = 90.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
xia2	data reduction
MrBUMP	phasing
HKL-3000	data collection
PDB_EXTRACT	data extraction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Cheng, X.Y., Wei, Q.Y., Huang, Y., Su, Z.D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection