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Crystal structure of human MDM2 complexed with D-peptide (12 residues)

Analyse Crystal structure of human MDM2 complexed with D-peptide (12 residues) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IWY
Type: protein
Length: 189 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-peptide inhibitor; E3 ubiquitin-protein ligase MDM2
EC: 6.3.2.-
UniProt: Q00987
Pockets: 1 · best druggability 0.32

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	D-peptide inhibitor	protein	12	58% helix, 0% strand	—
A	E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-)	protein	82	48% helix, 11% strand	Q00987
C	E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-)	protein	83	47% helix, 18% strand	Q00987

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	50	0.32	0.77	13	empty

Interfaces

6 interfaces between chains.

A–C · 681 Å² buried · 4 hydrogen bonds · protein-protein
D–C · 596 Å² buried · 2 hydrogen bonds · protein-protein
B–A · 586 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 176 Å² buried · 6 hydrogen bonds · protein-protein
D–A · 134 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 d-amino (D-amino acid).

Compared structures

3IWY · Crystal structure of human MDM2 complexed with D-peptide (12 residues) · the same entry in another collection · chain B against B, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q00987
Elsewhere: RCSB PDB 3IWY · PDBe 3IWY · UniProt Q00987

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