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Crystal structure of a novel zen lactonase mutant with ligand Z

Analyse Crystal structure of a novel zen lactonase mutant with ligand Z in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XO8
Type: protein
Length: 2,104 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactonase for protein
UniProt: A0A0D2ILK1
Ligands: ZER
Pockets: 16 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, F	Lactonase for protein	protein	263	48% helix, 18% strand	A0A0D2ILK1
D	Lactonase for protein	protein	264	48% helix, 18% strand	A0A0D2ILK1
G	Lactonase for protein	protein	262	47% helix, 18% strand	A0A0D2ILK1
H	Lactonase for protein	protein	263	46% helix, 18% strand	A0A0D2ILK1

Ligands and binding sites

ZER · (3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.83	0.96	27	ZER
2	171	0.82	0.97	27	ZER
3	159	0.82	0.97	25	ZER
4	163	0.81	0.96	25	ZER
5	183	0.81	0.95	28	ZER

Interfaces

9 interfaces between chains.

A–C · 679 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 666 Å² buried · 8 hydrogen bonds · protein-protein
E–H · 665 Å² buried · 8 hydrogen bonds · protein-protein
F–G · 651 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 342 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5XO8 · Crystal structure of a novel ZEN lactonase mutant with ligand Z · the same entry in another collection · chain D against D, 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 A0A0D2ILK1
Elsewhere: RCSB PDB 5XO8 · PDBe 5XO8 · UniProt A0A0D2ILK1

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