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Coupling of active site motions and RNA binding

Analyse Coupling of active site motions and RNA binding in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1ZL3
Type
protein + RNA
Length
324 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FLO) UP*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'; TRNA…
EC
4.2.1.70
UniProt
P60340
Ligands
SO4
Pockets
2 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 35% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FLO) UP*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'rna22——
ATRNA pseudouridine synthase B (EC 4.2.1.70)protein30228% helix, 35% strandP60340

Ligands and binding sites

  • SO4 · Sulfate ion · ion · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13590.560.7632empty
2680.300.7417empty

Interfaces

1 interface between chains.

  • B–A · 1483 Ų buried · 50 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

  • 1ZL3 · Coupling of active site motions and RNA binding · the same entry in another collection · chain B against B, TM-score 1.00
  • P60340 · AlphaFold monomer V2.0 prediction for tRNA pseudouridine synthase B (P60340) · a predicted model of the same protein · chain A against A, TM-score 1.00

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