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Lam domain of human LARP1 in complex with aaa RNA

Analyse Lam domain of human LARP1 in complex with aaa RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7SOR
Type
protein + RNA
Length
184 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Isoform 2 of la-related protein 1; RNA (5'-R(*AP*AP*A)-3')
Ligands
CL
Pockets
1 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, CIsoform 2 of la-related protein 1protein8951% helix, 11% strand—
B, DRNA (5'-R(*AP*AP*A)-3')rna3——

Ligands and binding sites

  • CL · Chloride ion · ion · chains A, C
  • EDO · 1,2-ethanediol · additive · 2 copies · chains A, C

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1950.600.8818CL

Interfaces

6 interfaces between chains.

  • A–C · 450 Ų buried · 2 hydrogen bonds · protein-protein
  • A–B · 379 Ų buried · 11 hydrogen bonds · protein-nucleic
  • C–D · 359 Ų buried · 11 hydrogen bonds · protein-nucleic
  • A–D · 26 Ų buried · 0 hydrogen bonds · protein-nucleic
  • B–C · 22 Ų buried · 0 hydrogen bonds · protein-nucleic

Compared structures

  • 7SOR · LaM domain of human LARP1 in complex with AAA RNA · the same entry in another collection · chain A against A, TM-score 1.00

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