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The 1.7A crystal structure of mdmx with a stapled peptide, atsp-7041

Analyse The 1.7A crystal structure of mdmx with a stapled peptide, atsp-7041 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4N5T
Type: protein
Length: 102 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein MDM4; Atsp-7041 stapled-peptide
UniProt: Q7ZUW7
Ligands: ACE, 0EH, 2JH
Pockets: 1 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein MDM4	protein	90	43% helix, 18% strand	Q7ZUW7
B	Atsp-7041 stapled-peptide	protein	12	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains B
0EH · (2R)-2-amino-2-methylnonanoic acid · ligand · chains A, B
2JH · 3-cyclobutyl-L-alanine · ligand · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.43	0.83	14	2JH

Interfaces

1 interface between chains.

A–B · 565 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent, 1 modified (covalent ligand, nonstandard).

Compared structures

4N5T · The 1.7A Crystal Structure of MDMX with a Stapled Peptide, ATSP-7041 · the same entry in another collection · chain A against A, TM-score 1.00
Q7ZUW7 · AlphaFold monomer V2.0 prediction for protein MDM4 (Q7ZUW7) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q7ZUW7
Elsewhere: RCSB PDB 4N5T · PDBe 4N5T · UniProt Q7ZUW7

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