7QDQ: HDM2

Crystal Structure of HDM2 in complex with Caylin-1. Determined by X-ray diffraction at 1.26 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 1.26 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,084
Mol. weight: 11.83 kDa
Ligands: AU0
Released: 5 Oct 2022

Explore 7QDQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QDQ 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	32-41	10
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	107-109	3	1

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>7QDQ_1 E3 ubiquitin-protein ligase Mdm2 (chains A)
PASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSN
DLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN

Ligands and cofactors

ID	Name	Formula	Copies
AU0	Caylin-1	C30 H28 Cl4 N4 O4	1

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

Primary citation

Elucidation of a nutlin-derivative-HDM2 complex structure at the interaction site by NMR molecular replacement: A straightforward derivation. Mertens, V., Abi Saad, M.J., Coudevylle, N. et al. J Magn Reson Open (2022) 10-11:100032. DOI 10.1016/j.jmro.2022.100032

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
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…

Browse structure collections

About this viewer

MolViewer shows 7QDQ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.