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Crystal structure of the MZM-REP domains of Mind bomb 1

Analyse Crystal structure of the MZM-REP domains of Mind bomb 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XI6
Type: protein
Length: 363 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.04
Source: Homo sapiens
Molecule: E3 ubiquitin-protein ligase MIB1
EC: 6.3.2.-
UniProt: Q86YT6
Ligands: ZN, SO4
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · resolution 2.04 · 1 distinct chain · 15% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase MIB1 (EC 6.3.2.-)	protein	363	15% helix, 36% strand	Q86YT6

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	905	0.77	0.80	74	empty
2	140	0.50	0.79	23	SO4

Compared structures

4XI6 · Crystal structure of the mzm-rep domains of mind bomb 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q86YT6 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase MIB1 (Q86YT6) · a predicted model of the same protein · chain A against A, TM-score 0.81

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 Q86YT6
Elsewhere: RCSB PDB 4XI6 · PDBe 4XI6 · UniProt Q86YT6

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