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Structure of the quorum quenching lactonase from alicyclobacillus acidoterrestris bound to a glycerol molecule

Analyse Structure of the quorum quenching lactonase from alicyclobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CH0
Type: protein
Length: 825 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
UniProt: T0BMH6
Ligands: CO
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, F, I	Beta-lactamase	protein	275	27% helix, 29% strand	T0BMH6

Ligands and binding sites

CO · Cobalt (II) ion · metal · 6 copies · chains C, F, I
PG4 · Tetraethylene glycol · additive · 5 copies · chains C, F, I
GOL · Glycerol · additive · 3 copies · chains C, F, I
EDO · 1,2-ethanediol · additive · 2 copies · chains C

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	221	0.64	0.82	30	GOL
2	194	0.62	0.82	21	GOL
3	201	0.61	0.82	26	GOL
4	147	0.56	0.81	20	empty
5	152	0.41	0.74	26	empty

Interfaces

2 interfaces between chains.

F–I · 738 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 614 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6CH0 · Structure of the Quorum Quenching lactonase from Alicyclobacillus acidoterrestris bound… · the same entry in another collection · chain C against C, TM-score 1.00

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Every structure of UniProt T0BMH6
Elsewhere: RCSB PDB 6CH0 · PDBe 6CH0 · UniProt T0BMH6

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