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MolNFT v1 · #14427 · protein + RNA

Crystal structure of the pumilio-homology domain from human PUMILIO1 in complex with NRE1-14 RNA

1M8X · 5'-R(P*UP*UP*GP*UP*AP*UP*AP*U)-3': “Crystal structure of the pumilio-homology domain from human PUMILIO1 in complex with NRE1-14 RNA”. X-ray diffraction, 2 pockets (best druggability 0.50). MolNFT v1 #14427 on GenesisL1: 3D…

PDB
1M8X
Type
protein + RNA
Length
697 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-R(P*UP*UP*GP*UP*AP*UP*AP*U)-3'; 5'-R(P*UP*GP*UP*AP*UP*AP*U)-3'; Pumilio 1
UniProt
Q14671
Pockets
2 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 72% helix, 1% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
C5'-R(P*UP*UP*GP*UP*AP*UP*AP*U)-3'rna8——
D5'-R(P*UP*GP*UP*AP*UP*AP*U)-3'rna7——
A, BPumilio 1protein34172% helix, 1% strandQ14671

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12070.500.7625empty
22230.490.7526empty

Interfaces

3 interfaces between chains.

  • D–B · 1180 Ų buried · 33 hydrogen bonds · protein-nucleic
  • C–A · 1148 Ų buried · 36 hydrogen bonds · protein-nucleic
  • A–B · 319 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

  • 1M8X · Crystal structure of the pumilio-homology domain from human PUMILIO1 in complex with… · the same entry in another collection · chain C against C, TM-score 1.00
  • Q14671 · AlphaFold monomer V2.0 prediction for pumilio homolog 1 (Q14671) · a predicted model of the same protein · chain A against A, TM-score 0.99

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