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The crystal structure of inactive dimeric peptidyl-tRNA hydrolase from acinetobacter baumannii at 1.79 a resolution

Analyse The crystal structure of inactive dimeric peptidyl-tRNA hydrolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YL8
Type: protein
Length: 386 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: D0C9L6
Ligands: NA
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peptidyl-tRNA hydrolase (EC 3.1.1.29)	protein	193	40% helix, 22% strand	D0C9L6

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	142	0.51	0.80	30	empty
2	110	0.49	0.81	21	empty
3	71	0.29	0.73	21	empty

Interfaces

1 interface between chains.

A–B · 550 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5YL8 · The crystal structure of inactive dimeric peptidyl-tRNA hydrolase from Acinetobacter… · the same entry in another collection · chain A against A, TM-score 1.00

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 D0C9L6
Elsewhere: RCSB PDB 5YL8 · PDBe 5YL8 · UniProt D0C9L6

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