8IA5: Protein Mdm4

Small peptide enhances the binding of nutline-3a to N-terminal domain of MdmX. Determined by X-ray diffraction at 1.93 Å resolution. Released 22 Feb 2023.

Method: X-ray diffraction
Resolution: 1.93 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 890
Mol. weight: 12.19 kDa
Ligands: NUT, O4B
Released: 22 Feb 2023

Explore 8IA5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IA5 contains 5 α-helices and 7 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
β-strand	27-28	2	2
α-helix	30-38	9
β-strand	46-47	2	1
α-helix	48-61	14
β-strand	65	1	3
β-strand	72-74	3	3
α-helix	79-84	6
β-strand	88-90	3	3
α-helix	95-104	10
β-strand	105-106	2	2

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein Mdm4	A	protein	90	Homo sapiens	O15151 (AlphaFold model)
9-mer peptide	B	protein	9	synthetic construct

Sequence of entity 1 (A), FASTA

>8IA5_1 Protein Mdm4 (chains A)
SQINQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLL
GELLGRQSFSVKDPSPLYDMLRKNLVTLAT

Sequence of entity 2 (B), FASTA

>8IA5_2 9-mer peptide (chains B)
DLENLYFQG

Ligands and cofactors

ID	Name	Formula	Copies
NUT	4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-…	C30 H30 Cl2 N4 O4	1
O4B	1,4,7,10,13,16-hexaoxacyclooctadecane	C12 H24 O6	1

Primary citation

Small peptide enhances the binding of nutline-3a to N-terminal domain of MdmX. Cheng, X.Y., Wei, Q.Y., Huang, Y. et al. To be published.

Other PDB entries of the same protein (UniProt O15151 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q9Y 1.2 Å, HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 16 AT 1.20A; Structural states of Hdm2 and…
3FEA 1.33 Å, Crystal Structure of HdmX bound to the p53-peptidomimetic…
3FE7 1.35 Å, Crystal Structure of HdmX bound to the p53-peptidomimetic…
3FDO 1.4 Å, Structure of human MDMX in complex with high affinity peptide
3LBJ 1.5 Å, Structure of human MDMX protein in complex with a small molecule inhibitor
4RXZ 1.55 Å, Crystal Structure of MDMX phosporylated Tyr99 in complex with a 12-mer peptide
6Q9W 1.55 Å, X-ray structure of compound 15 bound to HdmX: Structural states of Hdm2 and HdmX: X-ray…
3EQY 1.63 Å, Crystal structure of human MDMX in complex with a 12-mer peptide inhibitor
7C3Y 1.63 Å, Crystal structure of the N-terminal domain of human MdmX protein in complex with Nutlin3a
7C44 1.65 Å, Crystal structure of the p53-binding domain of human MdmX protein in complex with Nutlin3a
8HDG 1.73 Å, Small peptide enhances the binding of nutline-3a to MdmX
3JZP 1.74 Å, Human MDMX liganded with a 12mer peptide inhibitor (pDI6W)

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