8P41 | pdb_00008p41

Crystal structure of glucocerebrosidase in complex with allosteric activator

PDB DOI: https://doi.org/10.2210/pdb8P41/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2023-05-18 Released: 2024-03-06
Deposition Author(s): Schulze, M.-S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.238 (Depositor)
R-Value Work:
0.204 (Depositor)
R-Value Observed:
0.206 (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

Identification of ss-Glucocerebrosidase Activators for Glucosylceramide hydrolysis.

Schulze, M.E.D., Scholz, D., Jnoff, E., Hall, A., Melin, J., Sands, Z.A., Rodriguez, E., Andre, V.M.

(2024) ChemMedChem 19: e202300548-e202300548

PubMed: 38381042 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.202300548
Primary Citation Related Structures:
8P3E, 8P41

PubMed Abstract:
Several novel chemical series were identified that modulate glucocerebrosidase (GCase). Compounds from these series are active on glucosylceramide, unlike other known GCase modulators. We obtained GCase crystal structures with two compounds that have distinct chemotypes. Positive allosteric modulators bind to a site on GCase and induce conformational changes, but also induce an equilibrium state between monomer and dimer.

Organizational Affiliation

UCB, 216 Bath Road, Slough, SL1 3WE, UK.

Macromolecule Content

Total Structure Weight: 114.41 kDa
Atom Count: 8,510
Modeled Residue Count: 994
Deposited Residue Count: 994
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylceramidase	A, B	497	Homo sapiens	Mutation(s): 0 Gene Names: GBA, GC, GLUC EC: 3.2.1.45 (PDB Primary Data), 2.4.1 (PDB Primary Data), 3.2.1.104 (PDB Primary Data), 3.2.1.46 (UniProt), 3.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04062 (Homo sapiens) Explore P04062 Go to UniProtKB: P04062
PHAROS: P04062 GTEx: ENSG00000177628
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04062
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P04062-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WYC (Subject of Investigation/LOI) Query on WYC Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A]	2-[2-[[3,5-bis(trifluoromethyl)phenyl]methylsulfanyl]ethanoylamino]-5-chloranyl-benzoic acid C₁₈ H₁₂ Cl F₆ N O₃ S KDPCUGVFKIBQOY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] 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 T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain S [auth B] SDF format, chain J [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] 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 T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] 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 T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]