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Crystal structure of Mmi1 YTH domain complex with RNA

Analyse Crystal structure of Mmi1 YTH domain complex with RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DNO
Type: protein + RNA
Length: 171 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.8
Source: Schizosaccharomyces pombe 972h-; SYNTHETIC CONSTRUCT
Molecule: YTH domain-containing protein mmi1; RNA (5'-R(*CP*UP*UP*AP*AP*AP*C)-3')
UniProt: O74958
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · resolution 1.8 · 2 distinct chains · 29% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YTH domain-containing protein mmi1	protein	164	29% helix, 32% strand	O74958
B	RNA (5'-R(CPUPUPAPAPAP*C)-3')	rna	7	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.47	0.84	18	empty
2	57	0.29	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 634 Å² buried · 26 hydrogen bonds · protein-nucleic

Compared structures

5DNO · Crystal structure of MMI1 yth domain complex with RNA · the same entry in another collection · chain A against A, TM-score 1.00
O74958 · AlphaFold monomer V2.0 prediction for RNA binding exosome specificity factor MMI1 (O74958) · 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 O74958
Elsewhere: RCSB PDB 5DNO · PDBe 5DNO · UniProt O74958

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