3WF2

Crystal structure of human beta-galactosidase in complex with NBT-DGJ

PDB DOI: https://doi.org/10.2210/pdb3WF2/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.240
R-Value Work: 0.175
R-Value Observed: 0.178

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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.

Macromolecule Content

Total Structure Weight: 312.53 kDa
Atom Count: 20,707
Modelled Residue Count: 2,416
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, D	678	Homo sapiens	Mutation(s): 0 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 GTEx: ENSG00000170266
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16278
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P16278-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDJ Query on NDJ Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain J [auth A] SDF format, chain PA [auth D] SDF format, chain T [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain T [auth B]	CA [auth C], J [auth A], PA [auth D], T [auth B]	(2R,3S,4R,5S)-N-butyl-3,4,5-trihydroxy-2-(hydroxymethyl)piperidine-1-carbothioamide C₁₁ H₂₂ N₂ O₄ S VCRXDLDGTLMSHK-XFWSIPNHSA-N		Interactions Focus chain CA [auth C] Focus chain J [auth A] Focus chain PA [auth D] Focus chain T [auth B] Interactions & Density Focus chain CA [auth C] Focus chain J [auth A] Focus chain PA [auth D] Focus chain T [auth B]
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 G [auth A] SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [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 Y [auth C] SDF format, chain Z [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 G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [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 Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [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], KA [auth D], LA [auth D], MA [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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain IA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain IA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	DA [auth C] EA [auth C] K [auth A] L [auth A] QA [auth D] DA [auth C], EA [auth C], K [auth A], L [auth A], QA [auth D], RA [auth D], U [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	GA [auth C] HA [auth C] M [auth A] N [auth A] NA [auth D] GA [auth C], HA [auth C], M [auth A], N [auth A], NA [auth D], OA [auth D], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain W [auth B] Focus chain X [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain I [auth A] SDF format, chain JA [auth D] SDF format, chain S [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain S [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain S [auth B]	FA [auth C], I [auth A], JA [auth D], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth C] Focus chain I [auth A] Focus chain JA [auth D] Focus chain S [auth B] Interactions & Density Focus chain FA [auth C] Focus chain I [auth A] Focus chain JA [auth D] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.240
R-Value Work: 0.175
R-Value Observed: 0.178
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.119	α = 90
b = 116.26	β = 92.41
c = 141.768	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: 2014-04-16

Deposition Author(s):

Suzuki, H.

Ohto, U.

Shimizu, T.

Revision History (Full details and data files)

Version 1.0: 2014-04-16
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-10-09
Changes: Structure summary