3WEZ | pdb_00003wez

Crystal structure of human beta-galactosidase in complex with NOEV

PDB DOI: https://doi.org/10.2210/pdb3WEZ/pdb

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

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: 2.11 Å
R-Value Free:
0.225 (Depositor), 0.180 (DCC)
R-Value Work:
0.179 (Depositor), 0.181 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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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: 312.57 kDa
Atom Count: 21,184
Modeled Residue Count: 2,415
Deposited Residue Count: 2,712
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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
N8V Query on N8V Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain NA [auth D] SDF format, chain J [auth A] SDF format, chain DA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain DA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain DA [auth C]	DA [auth C], J [auth A], NA [auth D], T [auth B]	(1S,2S,3S,6R)-4-(hydroxymethyl)-6-(octylamino)cyclohex-4-ene-1,2,3-triol C₁₅ H₂₉ N O₄ UPZUHYMBTUUPML-QPSCCSFWSA-N		Interactions Focus chain DA [auth C] Focus chain J [auth A] Focus chain NA [auth D] Focus chain T [auth B] Interactions & Density Focus chain DA [auth C] Focus chain J [auth A] Focus chain NA [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 O [auth B] SDF format, chain R [auth B] SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain LA [auth D] SDF format, chain KA [auth D] SDF format, chain JA [auth D] SDF format, chain IA [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] 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 O [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] 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 O [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain LA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	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		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 JA [auth D] Focus chain KA [auth D] Focus chain LA [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 JA [auth D] Focus chain KA [auth D] Focus chain LA [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 V [auth B] SDF format, chain U [auth B] SDF format, chain PA [auth D] SDF format, chain OA [auth D] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain FA [auth C] SDF format, chain EA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C]	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], U [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain U [auth B] Focus chain V [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth C]	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], 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 QA [auth D] Focus chain RA [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 QA [auth D] Focus chain RA [auth D] Focus chain W [auth B] Focus chain X [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain I [auth A] SDF format, chain S [auth B] SDF format, chain MA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] MOL2 format, chain MA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain S [auth B] mmCIF format, chain MA [auth D]	CA [auth C], I [auth A], MA [auth D], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain I [auth A] Focus chain MA [auth D] Focus chain S [auth B] Interactions & Density Focus chain CA [auth C] Focus chain I [auth A] Focus chain MA [auth D] Focus chain S [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
N8V	BindingDB: 3WEZ	Ki: min: 300, max: 510 (nM) from 2 assay(s)
N8V	BindingDB: 3WEZ	IC50: 125 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.225 (Depositor), 0.180 (DCC)
R-Value Work: 0.179 (Depositor), 0.181 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.933	α = 90
b = 115.915	β = 92.25
c = 140.51	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

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Ligand Structure Quality Assessment

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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
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-11-13
Changes: Structure summary