MolNFT v1 · #142218 · protein

Crystal structure of peptidyl-tRNA hydrolase from thermus thermophilus

5ZX8: “Crystal structure of peptidyl-tRNA hydrolase from thermus thermophilus”. X-ray diffraction, 1 pocket (best druggability 0.30). MolNFT v1 #142218 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZX8
Type: protein
Length: 186 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: Q5SHZ2
Pockets: 1 · best druggability 0.30

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidyl-tRNA hydrolase (EC 3.1.1.29)	protein	186	42% helix, 21% strand	Q5SHZ2

Ligands and binding sites

FLC · Citrate anion · additive · 2 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.30	0.75	17	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5ZX8 · Crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
Q5SHZ2 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (Q5SHZ2) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q5SHZ2
Elsewhere: RCSB PDB 5ZX8 · PDBe 5ZX8 · UniProt Q5SHZ2

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