8F13: MDM2 P53 binding domain

Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon Polypeptide, alternative C-terminus. Determined by X-ray diffraction at 1.4 Å resolution. Released 15 Feb 2023.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,175
Mol. weight: 13.81 kDa
Ligands: WHL
Released: 15 Feb 2023

Explore 8F13 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F13 contains 7 α-helices and 6 β-strands across 2 chains. 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: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	21-23	3
β-strand	27-30	4	1
α-helix	32-39	8
β-strand	48-49	2	1
α-helix	50-64	15
β-strand	67	1	2
β-strand	74-76	3	2
α-helix	81-86	6
β-strand	90-92	3	2
α-helix	96-104	9
β-strand	107-109	3	1

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-15	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A	protein	95	Homo sapiens	Q00987 (AlphaFold model)
H103	B	protein	19	synthetic construct

Sequence of entity 1 (A), FASTA

>8F13_1 E3 ubiquitin-protein ligase Mdm2 (chains A)
SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVY
CSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN

Sequence of entity 2 (B), FASTA

>8F13_2 H103 (chains B)
XDPAWYECLEAALLCQQVX

Ligands and cofactors

ID	Name	Formula	Copies
WHL	N,N'-(1,4-phenylene)diacetamide	C10 H12 N2 O2	1

Water and common crystallization additives (DMS, SO4, EDO) are not listed.

Primary citation

Single-Shot Flow Synthesis of D-Proteins for Mirror-Image Phage Display. Callahan, A.J., Gandhesiri, S., Travaline, T.L. et al. ChemRxiv (2023). DOI 10.26434/chemrxiv-2023-x86xp

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
8J81 1.35 Å, MDM2 bound with a peptoid
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)

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