5DMY

Beta-galactosidase - construct 33-930

PDB DOI: https://doi.org/10.2210/pdb5DMY/pdb

Classification: HYDROLASE
Organism(s): Bifidobacterium bifidum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-09-09 Released: 2016-10-05
Deposition Author(s): Watson, K.A., Lazidou, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.264
R-Value Work: 0.198
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

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

Literature

Rational protein engineering toward the development of a beta-galactosidase with improved functional properties

Lazidou, A., Charalampopoulos, D., Watson, K.A.

To be published.

Macromolecule Content

Total Structure Weight: 294.57 kDa
Atom Count: 21,901
Modelled Residue Count: 2,568
Deposited Residue Count: 2,712
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C	904	Bifidobacterium bifidum	Mutation(s): 0 Gene Names: bbgIII EC: 3.2.1.23
UniProt
Find proteins for D4QAP3 (Bifidobacterium bifidum) Explore D4QAP3 Go to UniProtKB: D4QAP3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D4QAP3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C]	D [auth A], E [auth A], J [auth B], K [auth B], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain F [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain F [auth A]	F [auth A], M [auth C], N [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain M [auth C] Focus chain N [auth C]