8J81: MDM2

MDM2 bound with a peptoid. Determined by X-ray diffraction at 1.35 Å resolution. Released 1 May 2024.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Homo sapiens
Chains: 1
Atoms: 945
Mol. weight: 12.61 kDa
Ligands: UAC
Released: 1 May 2024

Explore 8J81 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J81 contains 4 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	1
α-helix	32-40	9
β-strand	48-49	2	1
α-helix	50-63	14
β-strand	67-68	2	2
β-strand	71-76	6	2
α-helix	81-86	6
β-strand	90-92	3	2
α-helix	96-104	9
β-strand	107-110	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A	protein	100	Homo sapiens	Q00987 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8J81_1 E3 ubiquitin-protein ligase Mdm2 (chains A)
GPLGSSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQ
QHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN

Ligands and cofactors

ID	Name	Formula	Copies
UAC	(2S)-2-[[(2S)-2-[(6-chloranyl-1H-indol-3-yl)methyl-[(2S)-2-[[(2S)-2-[ethanoyl-(…	C45 H65 Cl N8 O6	1

Water and common crystallization additives (CL) are not listed.

Primary citation

A high-resolution structural characterization and physicochemical study of how a peptoid binds to an oncoprotein MDM2. Yokomine, M., Morimoto, J., Fukuda, Y. et al. Chem Sci (2024) 15:7051-7060. DOI 10.1039/d4sc01540a · PubMed

Other PDB entries of the same protein (UniProt Q00987 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q9L 1.13 Å, HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2…
5C5A 1.15 Å, Crystal Structure of HDM2 in complex with Nutlin-3a
6Q9O 1.21 Å, HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 10 AT 1.21A; Structural states of Hdm2…
5ZXF 1.25 Å, The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a
7QDQ 1.26 Å, Crystal Structure of HDM2 in complex with Caylin-1
8F10 1.28 Å, Structure of the MDM2 P53 binding domain in complex with H102, an all-D Helicon…
8P0D 1.31 Å, Human 14-3-3 sigma in complex with human MDM2 peptide
5Z02 1.35 Å, Crystal structure of HIS6-tagged Mdm2 with nutlin-3a
4OGN 1.38 Å, Co-Crystal Structure of MDM2 with Inhbitor Compound 3
2AXI 1.4 Å, HDM2 in complex with a beta-hairpin
7KJM 1.4 Å, Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-omega)
8F13 1.4 Å, Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon…

Browse structure collections

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