5ZXF: The 1.25A Crystal structure of His6-tagged Mdm2

The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a. Determined by X-ray diffraction at 1.25 Å resolution. Released 22 Aug 2018.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 1
Atoms: 797
Mol. weight: 10.85 kDa
Ligands: NUT
Released: 22 Aug 2018

Explore 5ZXF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZXF contains 5 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: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	6-9	4	1
α-helix	11-19	9
β-strand	27-28	2	1
α-helix	29-42	14
β-strand	46	1	2
β-strand	53-55	3	2
α-helix	60-65	6
β-strand	69-71	3	2
α-helix	75-83	9
β-strand	86-88	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A	protein	87	Homo sapiens	Q00987 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5ZXF_1 E3 ubiquitin-protein ligase Mdm2 (chains A)
QETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLG
DLFGVPSFSVKEHRKIYTMIYRNLVVV

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

Primary citation

The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a. Cheng, X.Y., Su, Z.D. To be published.

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…
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)
8F13 1.4 Å, Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon…

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