5C5A: HDM2

Crystal Structure of HDM2 in complex with Nutlin-3a. Determined by X-ray diffraction at 1.15 Å resolution. Released 29 Jun 2016.

Method: X-ray diffraction
Resolution: 1.15 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,842
Mol. weight: 23.47 kDa
Ligands: NUT
Released: 29 Jun 2016

Explore 5C5A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C5A contains 8 α-helices and 12 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.

Chains A and B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	1
α-helix	32-41	10
β-strand	48-49	2	1
α-helix	50-64	15
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	107-109	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A, B	protein	92	Homo sapiens	Q00987 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5C5A_1 E3 ubiquitin-protein ligase Mdm2 (chains A, B)
PASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSN
DLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN

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	2

Water and common crystallization additives (IOD, CL, SO4) are not listed.

Primary citation

NMR Molecular Replacement, NMR2. Orts, J., Waelti, M.A., Marsh, M. et al. 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…
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)
8F13 1.4 Å, Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon…

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