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Crystal structure of human pumilio 1 in complex with PUF5 RNA

Analyse Crystal structure of human pumilio 1 in complex with PUF5 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3BSX
Type
protein + RNA
Length
700 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Pumilio homolog 1; 5'-R(*UP*UP*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'
UniProt
Q14671
Pockets
2 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APumilio homolog 1protein34174% helix, 0% strandQ14671
BPumilio homolog 1protein34073% helix, 0% strandQ14671
C5'-R(*UP*UP*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'rna10——
D5'-R(*UP*UP*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'rna9——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1880.560.8625empty
2780.330.7416empty

Interfaces

4 interfaces between chains.

  • A–C · 1389 Ų buried · 40 hydrogen bonds · protein-nucleic
  • B–D · 1358 Ų buried · 39 hydrogen bonds · protein-nucleic
  • A–B · 577 Ų buried · 4 hydrogen bonds · protein-protein
  • A–D · 61 Ų buried · 0 hydrogen bonds · protein-nucleic

Compared structures

  • 3BSX · Crystal Structure of Human Pumilio 1 in complex with Puf5 RNA · the same entry in another collection · chain A against A, TM-score 1.00
  • Q14671 · AlphaFold monomer V2.0 prediction for pumilio homolog 1 (Q14671) · a predicted model of the same protein · chain B against A, TM-score 0.99

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