8F10 | pdb_00008f10

Structure of the MDM2 P53 binding domain in complex with H102, an all-D Helicon Polypeptide

PDB DOI: https://doi.org/10.2210/pdb8F10/pdb

Classification: LIGASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free:
0.167 (Depositor), 0.172 (DCC)
R-Value Work:
0.154 (Depositor), 0.161 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 13.79 kDa
Atom Count: 1,062
Modeled Residue Count: 103
Deposited Residue Count: 114
Unique protein chains: 2

Macromolecules

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| 3D Structure

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) Explore Q00987 Go to UniProtKB: Q00987
PHAROS: Q00987 GTEx: ENSG00000135679
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00987
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H102	B	19	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WHL Query on WHL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	N,N'-(1,4-phenylene)diacetamide C₁₀ H₁₂ N₂ O₂ KVEDKKLZCJBVNP-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth A], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth A] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 12 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL Query on DAL	B	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
DAS Query on DAS	B	D-PEPTIDE LINKING	C₄ H₇ N O₄		--
DCY Query on DCY	B	D-PEPTIDE LINKING	C₃ H₇ N O₂ S		--
DGL Query on DGL	B	D-PEPTIDE LINKING	C₅ H₉ N O₄		--
DHI Query on DHI	B	D-PEPTIDE LINKING	C₆ H₁₀ N₃ O₂		--
DPN Query on DPN	B	D-PEPTIDE LINKING	C₉ H₁₁ N O₂		--
DPR Query on DPR	B	D-PEPTIDE LINKING	C₅ H₉ N O₂		--
DSG Query on DSG	B	D-PEPTIDE LINKING	C₄ H₈ N₂ O₃		--
DSN Query on DSN	B	D-PEPTIDE LINKING	C₃ H₇ N O₃		--
DTR Query on DTR	B	D-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₂		--
DTY Query on DTY	B	D-PEPTIDE LINKING	C₉ H₁₁ N O₃		--
DVA Query on DVA	B	D-PEPTIDE LINKING	C₅ H₁₁ N O₂		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.167 (Depositor), 0.172 (DCC)
R-Value Work: 0.154 (Depositor), 0.161 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.15	α = 90
b = 39.92	β = 95.44
c = 42.36	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

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