9FQL | pdb_00009fql

Crystal structure of hDM2 in complex with a peptidic ligand containing a di-urea insert.

PDB DOI: https://doi.org/10.2210/pdb9FQL/pdb

Classification: ANTITUMOR PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-06-17 Released: 2025-07-02
Deposition Author(s): Buratto, J., Mauran, L., Goudreau, S., Guichard, G.
Funding Organization(s): Centre National de la Recherche Scientifique (CNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.248 (Depositor), 0.253 (DCC)
R-Value Work:
0.221 (Depositor), 0.225 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of hDM2 in complex with a peptidic ligand containing a di-urea insert.

Buratto, J., Mauran, L., Goudreau, S., Guichard, G.

To be published.

Macromolecule Content

Total Structure Weight: 69.53 kDa
Atom Count: 4,755
Modeled Residue Count: 576
Deposited Residue Count: 582
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B, E, F, I A, B, E, F, I, J	86	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
p25Lp26A	C, D, G, H, K C, D, G, H, K, L	11	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth I] SDF format, chain S [auth I] SDF format, chain T [auth J] SDF format, chain U [auth K] SDF format, chain V [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth I] MOL2 format, chain S [auth I] MOL2 format, chain T [auth J] MOL2 format, chain U [auth K] MOL2 format, chain V [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth I] mmCIF format, chain S [auth I] mmCIF format, chain T [auth J] mmCIF format, chain U [auth K] mmCIF format, chain V [auth L]	M [auth A] N [auth B] O [auth B] P [auth C] Q [auth D] M [auth A], N [auth B], O [auth B], P [auth C], Q [auth D], R [auth I], S [auth I], T [auth J], U [auth K], V [auth L]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth I] Focus chain S [auth I] Focus chain T [auth J] Focus chain U [auth K] Focus chain V [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth I] Focus chain S [auth I] Focus chain T [auth J] Focus chain U [auth K] Focus chain V [auth L]