4UE1: Stapled peptide YS-01

Structure of the stapled peptide YS-01 bound to MDM2. Determined by X-ray diffraction at 1.45 Å resolution. Released 13 Jan 2016.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: HOMO SAPIENS
Chains: 8
Atoms: 4,072
Mol. weight: 58.62 kDa
Released: 13 Jan 2016

Explore 4UE1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4UE1 contains 28 α-helices and 28 β-strands across 8 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	21-23	3
β-strand	25-27	3	1
β-strand	28	1	2
β-strand	30	1	3
α-helix	32-40	9
β-strand	48	1	2
α-helix	50-64	15
β-strand	67	1	4
β-strand	74-76	3	4
α-helix	81-86	6
β-strand	90-92	3	4
α-helix	96-104	9
β-strand	107	1	3

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	21-23	3
β-strand	25-27	3	1
β-strand	28	1	5
β-strand	30	1	6
α-helix	32-39	8
β-strand	48	1	5
α-helix	50-63	14
β-strand	67-68	2	7
β-strand	71-76	6	7
α-helix	81-86	6
β-strand	90-92	3	7
α-helix	96-104	9
β-strand	107	1	6

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	23-25	3
β-strand	27-30	4	8
α-helix	32-40	9
β-strand	48-49	2	8
α-helix	50-63	14
β-strand	67	1	9
β-strand	74-76	3	9
α-helix	81-86	6
β-strand	90-92	3	9
α-helix	96-104	9
β-strand	107-109	3	8

Chain D: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	23-25	3
β-strand	27-30	4	10
α-helix	32-41	10
β-strand	48-49	2	10
α-helix	50-63	14
β-strand	67	1	11
β-strand	74-76	3	11
α-helix	80-86	7
β-strand	90-92	3	11
α-helix	96-105	10
β-strand	107-109	3	10

Chains F and G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	19-29	11

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	19-24	6

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	19-25	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase MDM2	A, B, C, D	protein	114	HOMO SAPIENS	Q00987 (AlphaFold model)
YS-01	F, G, H, I	protein	16	HOMO SAPIENS

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

>4UE1_1 E3 UBIQUITIN-PROTEIN LIGASE MDM2 (chains A, B, C, D)
GPLGSSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQ
QHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSEN

Sequence of entity 2 (F, G, H, I), FASTA

>4UE1_2 YS-01 (chains F, G, H, I)
XTSFXEYWXLLPENFX

Primary citation

Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design. Tan, Y.S., Reeks, J., Brown, C.J. et al. J Phys Chem Lett (2016) 7:3452-3457. DOI 10.1021/acs.jpclett.6b01525 · PubMed

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
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)

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