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Crystal structure of the RNA-binding domain of yeast PUF5P bound to MFA2 RNA

Analyse Crystal structure of the RNA-binding domain of yeast PUF5P bound to MFA2 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BZ1
Type: protein + RNA
Length: 381 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Suppressor protein MPT5; RNA (5'-R(*UP*GP*UP*AP*UP*UP*UP*GP*UP*A)-3')
UniProt: P39016
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Suppressor protein MPT5	protein	371	77% helix, 0% strand	P39016
B	RNA (5'-R(UPGPUPAPUPUPUPGPUPA)-3')	rna	10	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.35	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 1354 Å² buried · 43 hydrogen bonds · protein-nucleic

Compared structures

5BZ1 · Crystal structure of the RNA-binding domain of yeast Puf5p bound to MFA2 RNA · the same entry in another collection · chain A against A, TM-score 1.00
P39016 · AlphaFold monomer V2.0 prediction for suppressor protein MPT5 (P39016) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P39016
Elsewhere: RCSB PDB 5BZ1 · PDBe 5BZ1 · UniProt P39016

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