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MolNFT v1 · #136832 · protein

Crystal structure of human prolyl-tRNA synthetase in complex with aze- sa

5V58 · Bifunctional GLUTAMATE/PROLINE--tRNA ligase: “Crystal structure of human prolyl-tRNA synthetase in complex with aze- sa”. X-ray diffraction, 2 ligands (8X1, ZN), 3 pockets (best druggability 0.70). MolNFT v1 #136832 on GenesisL1: 3D…

PDB
5V58
Type
protein
Length
476 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Bifunctional GLUTAMATE/PROLINE--tRNA ligase
EC
6.1.1.17, 6.1.1.15
UniProt
P07814
Ligands
8X1, ZN
Pockets
3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 29% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17, 6.1.1.15)protein47637% helix, 29% strandP07814

Ligands and binding sites

  • 8X1 · 5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine · ligand · chains A
  • ZN · Zinc ion · metal · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15570.700.79588X1
2910.440.7919empty
3540.410.8114empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

  • 5V58 · Crystal structure of human prolyl-tRNA synthetase in complex with Aze-SA · the same entry in another collection · chain A against A, TM-score 1.00
  • P07814 · AlphaFold monomer V2.0 prediction for bifunctional GLUTAMATE/PROLINE --tRNA ligase… · a predicted model of the same protein · chain A against A, TM-score 0.99

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