8H25

Lacticaseibacillus casei GH35 beta-galactosidase LBCZ_0230

PDB DOI: https://doi.org/10.2210/pdb8H25/pdb

Classification: HYDROLASE
Organism(s): Lacticaseibacillus casei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-04 Released: 2023-08-16
Deposition Author(s): Saburi, W., Ota, T., Kato, K., Tagami, T., Yamashita, K., Yao, M., Mori, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.232
R-Value Work: 0.195

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Function and structure of Lacticaseibacillus cases GH35 beta-galactosidase LBCZ_0230 with high hydrolytic activity to lactose-N-biose I and galactic-N-biose.

Saburi, W., Ota, T., Kato, K., Tagami, T., Yamashita, K., Yao, M., Mori, H.

(2023) J Appl Glycosci (1999) 70: 43-52

DOI: https://doi.org/10.5458/jag.jag.JAG-2022_0014

Macromolecule Content

Total Structure Weight: 277.08 kDa
Atom Count: 19,500
Modelled Residue Count: 2,368
Deposited Residue Count: 2,416
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	604	Lacticaseibacillus casei	Mutation(s): 0 Gene Names: FEI12_08385
UniProt
Find proteins for A0A5R8LFD3 (Lacticaseibacillus casei) Explore A0A5R8LFD3 Go to UniProtKB: A0A5R8LFD3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5R8LFD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D]	I [auth B], L [auth C], M [auth C], O [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth C]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth C] E [auth A], F [auth A], G [auth A], H [auth A], K [auth C], N [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]