MolNFT v1 · #114239 · protein

Crystal structure of peptidyl-tRNA hydrolase mutant -H24N from vibrio cholerae

5B6J: “Crystal structure of peptidyl-tRNA hydrolase mutant -H24N from vibrio cholerae”. X-ray diffraction, 3 pockets (best druggability 0.62). MolNFT v1 #114239 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B6J
Type: protein
Length: 392 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidyl-tRNA hydrolase
EC: 3.1.1.29
UniProt: A5F686
Pockets: 3 · best druggability 0.62

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peptidyl-tRNA hydrolase (EC 3.1.1.29)	protein	196	43% helix, 21% strand	A5F686

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	185	0.62	0.83	40	empty
2	116	0.49	0.80	27	empty
3	101	0.35	0.74	24	empty

Interfaces

1 interface between chains.

A–B · 959 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

5B6J · Crystal structure of Peptidyl-tRNA hydrolase mutant -H24N from Vibrio cholerae · 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

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 A5F686
Elsewhere: RCSB PDB 5B6J · PDBe 5B6J · UniProt A5F686

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