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MolNFT v1 · #138779 · protein + RNA

Structure of NOP9 RNA complex

5WTY · Nucleolar protein 9: “Structure of NOP9 RNA complex”. X-ray diffraction, 7 pockets (best druggability 0.59). MolNFT v1 #138779 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5WTY
Type
protein + RNA
Length
1,113 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Nucleolar protein 9; RNA (5'- R(*AP*AP*AP*GP*GP*AP*AP*UP*UP*GP*AP*CP*GP*GP*AP*AP*GP*G)-3')
UniProt
P47077
Pockets
7 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BNucleolar protein 9protein54770% helix, 0% strandP47077
ANucleolar protein 9protein54471% helix, 1% strandP47077
C, DRNA (5'- R(*AP*AP*AP*GP*GP*AP*AP*UP*UP*GP*AP*CP*GP*GP*AP*AP*GP*G)-3')rna11——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13450.590.7728empty
22480.480.7326empty
31410.440.7624empty
41330.390.7417empty
5970.340.7419empty

Interfaces

3 interfaces between chains.

  • B–D · 1674 Ų buried · 45 hydrogen bonds · protein-nucleic
  • A–C · 1611 Ų buried · 50 hydrogen bonds · protein-nucleic
  • B–A · 393 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

  • 5WTY · Structure of Nop9 RNA complex · the same entry in another collection · chain B against B, TM-score 1.00
  • P47077 · AlphaFold monomer V2.0 prediction for nucleolar protein 9 (P47077) · a predicted model of the same protein · chain B against A, TM-score 0.97

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