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Structure of T. thermophilus asprs in complex with 5'-O-(N-(L- aspartyl)-SULFAMOYL)N3-methyluridine

Analyse Structure of T. thermophilus asprs in complex with 5'-O-(N-(L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6HHV
Type
protein
Length
1,154 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Aspartate--TRNA(ASP) ligase
EC
6.1.1.12
UniProt
P36419
Ligands
G5Q
Pockets
13 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AAspartate--TRNA(ASP) ligase (EC 6.1.1.12)protein57433% helix, 26% strandP36419
BAspartate--TRNA(ASP) ligase (EC 6.1.1.12)protein58032% helix, 26% strandP36419

Ligands and binding sites

  • G5Q · 5'-O-(N-(L-aspartyl)-sulfamoyl)N3-methyluridine · ligand · 2 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11280.800.9722empty
26520.780.8472G5Q
34280.700.8152G5Q
4770.630.9022empty
51870.570.8035empty

Interfaces

1 interface between chains.

  • A–B · 5555 Ų buried · 83 hydrogen bonds · protein-protein

Compared structures

  • 6HHV · Structure of T. thermophilus AspRS in Complex with… · the same entry in another collection · chain A against A, TM-score 1.00
  • P36419 · AlphaFold monomer V2.0 prediction for aspartate--TRNA(ASP) ligase (P36419) · a predicted model of the same protein · chain B against A, TM-score 0.98

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