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Complex structure of the miwi paz domain bound to methylated single stranded RNA

Analyse Complex structure of the miwi paz domain bound to methylated single stranded RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XFM
Type: protein + RNA
Length: 128 residues
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Piwi-like protein 1; 5'-R(*AP*CP*CP*GP*AP*CP*UP*(OMU)P)-3'
UniProt: Q9JMB7
Pockets: 1 · best druggability 0.52

Structure

solution nmr · 2 distinct chains · 27% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Piwi-like protein 1	protein	120	27% helix, 18% strand	Q9JMB7
B	5'-R(APCPCPGPAPCPUP(OMU)P)-3'	rna	8	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	216	0.52	0.77	23	empty

Interfaces

1 interface between chains.

A–B · 725 Å² buried · 17 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

2XFM · Complex structure of the MIWI Paz domain bound to methylated single stranded RNA · the same entry in another collection · chain A against A, TM-score 1.00
Q9JMB7 · AlphaFold monomer V2.0 prediction for piwi-like protein 1 (Q9JMB7) · a predicted model of the same protein · chain A against A, TM-score 0.78

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 Q9JMB7
Elsewhere: RCSB PDB 2XFM · PDBe 2XFM · UniProt Q9JMB7

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