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Crystal structure of the KH2 domain of human RNA-binding E3 ubiquitin- protein ligase mex-3C complex with RNA

Analyse Crystal structure of the KH2 domain of human RNA-binding E3 ubiquitin- protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WWX
Type: protein + RNA
Length: 89 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding E3 ubiquitin-protein ligase MEX3C; RNA (5'-R(P*AP*GP*AP*GP*U)-3')
EC: 2.3.2.27
UniProt: Q5U5Q3
Ligands: NI

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-binding E3 ubiquitin-protein ligase MEX3C (EC 2.3.2.27)	protein	84	48% helix, 18% strand	Q5U5Q3
C	RNA (5'-R(PAPGPAPGP*U)-3')	rna	5	—	—

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A, C

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

Interfaces

1 interface between chains.

A–C · 696 Å² buried · 18 hydrogen bonds · protein-nucleic

Compared structures

5WWX · Crystal structure of the KH2 domain of human RNA-binding E3 ubiquitin-protein ligase… · the same entry in another collection · chain A against A, TM-score 1.00
Q5U5Q3 · AlphaFold monomer V2.0 prediction for RNA-binding E3 ubiquitin- protein ligase MEX3C… · a predicted model of the same protein · chain A against A, TM-score 0.88

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 Q5U5Q3
Elsewhere: RCSB PDB 5WWX · PDBe 5WWX · UniProt Q5U5Q3

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