8F13

Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon Polypeptide, alternative C-terminus

• PDB DOI: https://doi.org/10.2210/pdb8F13/pdb

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


• Deposited: 2022-11-04 Released: 2023-02-15 
• Deposition Author(s): Li, K., Callahan, A.J., Travaline, T.L., Tokareva, O.S., Swiecicki, J.-M., Verdine, G.L., Pentelute, B.L., McGee, J.H.
• Funding Organization(s): Other private, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 

Starting Model: experimental

Literature

Single-Shot Flow Synthesis of D-Proteins for Mirror-Image Phage Display

Callahan, A.J., Gandhesiri, S., Travaline, T.L., Lozano Salazar, L., Hanna, S., Lee, Y.-C., Li, K., Tokareva, O.S., Swiecicki, J.-M., Loas, A., Verdine, G.L., McGee, J.H., Pentelute, B.L.

(2023) ChemRxiv 

• DOI: https://doi.org/10.26434/chemrxiv-2023-x86xp

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 13.81 kDa 
• Atom Count: 1,175 
• Modelled Residue Count: 112 
• Deposited Residue Count: 114 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	95	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Go to UniProtKB:  Q00987
PHAROS:  Q00987 GTEx:  ENSG00000135679

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H103	B	19	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WHL	I [auth B]	N,N'-(1,4-phenylene)diacetamide C10 H12 N2 O2 KVEDKKLZCJBVNP-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.286	α = 90
b = 60.286	β = 90
c = 84.897	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Li, K., Callahan, A.J., Travaline, T.L., Tokareva, O.S., Swiecicki, J.-M., Verdine, G.L., Pentelute, B.L., McGee, J.H.

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Funding Organization	Location	Grant Number
Other private	United States	FOG Pharmaceuticals
Other private	United States	MIT School of Science Fellowship in Cancer Research
German Research Foundation (DFG)	Germany	LE 4224/1-1

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection