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Crystal structure of the MDM2-mdmx ring domain heterodimer

Analyse Crystal structure of the MDM2-mdmx ring domain heterodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VJE
Type: protein
Length: 243 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase MDM2; MDM4 protein
EC: 6.3.2.-
UniProt: Q00987, O15151
Ligands: ZN, SO4
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-)	protein	60	20% helix, 28% strand	Q00987
B	MDM4 protein	protein	61	21% helix, 36% strand	O15151
D	MDM4 protein	protein	62	23% helix, 35% strand	O15151

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · chains B, C, D
FLC · Citrate anion · additive · chains D

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	73	0.35	0.76	17	empty

Interfaces

4 interfaces between chains.

C–D · 1089 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1051 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 196 Å² buried · 1 hydrogen bond · protein-protein
B–D · 158 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2VJE · Crystal Structure of the MDM2-MDMX RING Domain Heterodimer · the same entry in another collection · chain A against A, TM-score 1.00
O15151 · AlphaFold monomer V2.0 prediction for protein MDM4 (O15151) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 Q00987
Every structure of UniProt O15151
Elsewhere: RCSB PDB 2VJE · PDBe 2VJE · UniProt Q00987 · UniProt O15151

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