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MolNFT v1 · #120306 · protein

Crystal structure of peptidyl-tRNA hydrolase from vibrio cholerae in space group C2221 at resolution 1.75A.

5GVZ: “Crystal structure of peptidyl-tRNA hydrolase from vibrio cholerae in space group C2221 at resolution 1.75A.”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.35). MolNFT v1 #120306 on GenesisL1: 3D structure…

PDB
5GVZ
Type
protein
Length
194 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Peptidyl-tRNA hydrolase
EC
3.1.1.29
UniProt
A5F686
Ligands
SO4
Pockets
1 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APeptidyl-tRNA hydrolase (EC 3.1.1.29)protein19443% helix, 21% strandA5F686

Ligands and binding sites

  • SO4 · Sulfate ion · ion · chains A
  • ACT · Acetate ion · additive · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1750.350.7623empty

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

  • 5GVZ · Crystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae in space group C2221 at… · the same entry in another collection · chain A against A, TM-score 1.00
  • A5F686 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (A5F686) · a predicted model of the same protein · chain A against A, TM-score 0.99

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