MolNFT v1 · #54135 · protein + RNA

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

2XFM · Piwi-like protein 1: “Complex structure of the miwi paz domain bound to methylated single stranded RNA”. Solution nmr, 1 pocket (best druggability 0.52). MolNFT v1 #54135 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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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