3WF3

Crystal structure of human beta-galactosidase mutant I51T in complex with Galactose

PDB DOI: https://doi.org/10.2210/pdb3WF3/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2013-07-16 Released: 2014-04-23
Deposition Author(s): Suzuki, H., Ohto, U., Shimizu, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.242
R-Value Work: 0.196
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of pharmacological chaperoning for human beta-galactosidase

Suzuki, H., Ohto, U., Higaki, K., Mena-Barragan, T., Aguilar-Moncayo, M., Ortiz Mellet, C., Nanba, E., Garcia Fernandez, J.M., Suzuki, Y., Shimizu, T.

To be published.

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, D	678	Homo sapiens	Mutation(s): 1 Gene Names: ELNR1, GLB1 EC: 3.2.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for P16278 (Homo sapiens) Explore P16278 Go to UniProtKB: P16278
PHAROS: P16278
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16278
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain Z [auth C] SDF format, chain G [auth A] SDF format, chain IA [auth D] SDF format, chain Y [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain Y [auth C]	AA [auth C], BA [auth C], E [auth A], F [auth A], G [auth A], AA [auth C], BA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], IA [auth D], JA [auth D], KA [auth D], LA [auth D], O [auth B], P [auth B], Q [auth B], R [auth B], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain NA [auth D] SDF format, chain X [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain X [auth B]	DA [auth C], I [auth A], NA [auth D], X [auth B]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain T [auth B] SDF format, chain EA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain U [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B]	EA [auth C], FA [auth C], K [auth A], L [auth A], OA [auth D], EA [auth C], FA [auth C], K [auth A], L [auth A], OA [auth D], PA [auth D], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain RA [auth D] SDF format, chain V [auth B] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain QA [auth D] SDF format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain W [auth B]	GA [auth C], HA [auth C], M [auth A], N [auth A], QA [auth D], GA [auth C], HA [auth C], M [auth A], N [auth A], QA [auth D], RA [auth D], V [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain J [auth A] SDF format, chain MA [auth D] SDF format, chain S [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain S [auth B]	CA [auth C], J [auth A], MA [auth D], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.242
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.96	α = 90
b = 115.888	β = 92.23
c = 140.284	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-04-23

Deposition Author(s):

Suzuki, H.

Ohto, U.

Shimizu, T.

Revision History (Full details and data files)

Version 1.0: 2014-04-23
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary