8HDG: Uncharacterized protein DKFZp686B01123

Small peptide enhances the binding of nutline-3a to MdmX. Determined by X-ray diffraction at 1.73 Å resolution. Released 30 Nov 2022.

Method: X-ray diffraction
Resolution: 1.73 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,483
Mol. weight: 54.32 kDa
Ligands: O4B, NUT
Released: 30 Nov 2022

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

Secondary structure: helices and β-sheets

8HDG contains 20 α-helices and 26 β-strands across 4 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	13-19	7
β-strand	26-27	2	3
β-strand	28-29	2	4
α-helix	31-39	9
β-strand	47-48	2	3
α-helix	49-62	14
β-strand	66	1	5
β-strand	73-75	3	5
α-helix	80-85	6
β-strand	89-91	3	5
α-helix	96-105	10
β-strand	106-107	2	4

Chains C and D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	13-19	7
β-strand	26-29	4	6
α-helix	31-39	9
β-strand	47-48	2	6
α-helix	49-62	14
β-strand	66	1	7
β-strand	73-75	3	7
α-helix	80-85	6
β-strand	89-91	3	7
α-helix	96-105	10
β-strand	106-108	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uncharacterized protein DKFZp686B01123	A, B, C, D	protein	111	Homo sapiens	O15151 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8HDG_1 Uncharacterized protein DKFZp686B01123 (chains A, B, C, D)
MGSSHHHHHHSQDLENLYFQGSQINQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYI
MVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLAT

Ligands and cofactors

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

Primary citation

Small peptide enhances the binding of nutline-3a to MdmX. Cheng, X.Y., Huang, Y., Wei, Q.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
3JZP 1.74 Å, Human MDMX liganded with a 12mer peptide inhibitor (pDI6W)
3JZO 1.8 Å, Human MDMX liganded with a 12mer peptide (pDI)

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