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MolNFT v1 · #5094 · protein + RNA

Crystal structure of the spliceosomal 15.5KD protein bound to a U4 snrna fragment

1E7K · 15.5 kd RNA binding protein: “Crystal structure of the spliceosomal 15.5KD protein bound to a U4 snrna fragment”. X-ray diffraction, 1 pocket (best druggability 0.68). MolNFT v1 #5094 on GenesisL1: 3D structure, binding sites and…

PDB
1E7K
Type
protein + RNA
Length
282 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
15.5 kd RNA binding protein; RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP*…
UniProt
P55769
Pockets
1 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A15.5 kd RNA binding proteinprotein12546% helix, 16% strandP55769
B15.5 kd RNA binding proteinprotein12346% helix, 16% strandP55769
C, DRNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3')rna17——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
16640.680.7753empty

Interfaces

4 interfaces between chains.

  • B–D · 677 Ų buried · 23 hydrogen bonds · protein-nucleic
  • A–C · 675 Ų buried · 26 hydrogen bonds · protein-nucleic
  • A–B · 365 Ų buried · 4 hydrogen bonds · protein-protein
  • B–C · 30 Ų buried · 0 hydrogen bonds · protein-nucleic

Compared structures

  • 1E7K · Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment · the same entry in another collection · chain D against D, TM-score 1.00
  • P55769 · AlphaFold monomer V2.0 prediction for NHP2-like protein 1 (P55769) · a predicted model of the same protein · chain B against A, TM-score 0.99

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