8AWR | pdb_00008awr

Structure of recombinant human beta-glucocerebrosidase in complex with L-carbaxylosyl chloride

PDB DOI: https://doi.org/10.2210/pdb8AWR/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2022-08-30 Released: 2024-03-13
Deposition Author(s): Rowland, R.J., Davies, G.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.222 (Depositor), 0.224 (DCC)
R-Value Work:
0.183 (Depositor), 0.185 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Single turnover covalent inhibitors for functional chaperoning of lysosomal glycoside hydrolases

Bhosale, S., Kandalkar, S., Gilormini, P.A., Akintola, O., Rowland, R.J., Adabala, P.J.P., King, D., Deen, M.C., Xi, K., Davies, G.J., Vocadlo, D.J., Bennet, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 58.93 kDa
Atom Count: 4,670
Modeled Residue Count: 497
Deposited Residue Count: 497
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysosomal acid glucosylceramidase	A [auth AAA]	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: 3	Glycosylation Focus chain A [auth AAA]	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
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth AcA]	4		N-Glycosylation	Interactions Focus chain B [auth AcA] Interactions & Density Focus chain B [auth AcA]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth AAA] SDF format, chain AA [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain AA [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain AA [auth AAA]	AA [auth AAA], L [auth AAA]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth AAA] Focus chain L [auth AAA] Interactions & Density Focus chain AA [auth AAA] Focus chain L [auth AAA]
OIZ (Subject of Investigation/LOI) Query on OIZ Download:Ideal Coordinates CCD File SDF format, chain Y [auth AAA] MOL2 format, chain Y [auth AAA] mmCIF format, chain Y [auth AAA]	Y [auth AAA]	(1~{S},2~{R},3~{S},6~{S})-6-chloranylcyclohex-4-ene-1,2,3-triol C₆ H₉ Cl O₃ CGZQOMOYCGJBIC-UNTFVMJOSA-N		Interactions Focus chain Y [auth AAA] Interactions & Density Focus chain Y [auth AAA]
OJ6 (Subject of Investigation/LOI) Query on OJ6 Download:Ideal Coordinates CCD File SDF format, chain Z [auth AAA] MOL2 format, chain Z [auth AAA] mmCIF format, chain Z [auth AAA]	Z [auth AAA]	(1~{S},2~{S},3~{S},4~{R})-cyclohexane-1,2,3,4-tetrol C₆ H₁₂ O₄ WESBWDZFWNIVRV-FSIIMWSLSA-N		Interactions Focus chain Z [auth AAA] Interactions & Density Focus chain Z [auth AAA]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain FA [auth AAA] MOL2 format, chain FA [auth AAA] mmCIF format, chain FA [auth AAA]	FA [auth AAA]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FA [auth AAA] Interactions & Density Focus chain FA [auth AAA]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA], D [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain X [auth AAA] SDF format, chain W [auth AAA] SDF format, chain V [auth AAA] SDF format, chain U [auth AAA] SDF format, chain T [auth AAA] SDF format, chain S [auth AAA] SDF format, chain R [auth AAA] SDF format, chain Q [auth AAA] SDF format, chain P [auth AAA] SDF format, chain O [auth AAA] SDF format, chain N [auth AAA] SDF format, chain M [auth AAA] SDF format, chain K [auth AAA] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] SDF format, chain EA [auth AAA] SDF format, chain E [auth AAA] SDF format, chain DA [auth AAA] SDF format, chain CA [auth AAA] SDF format, chain BA [auth AAA] MOL2 format, chain X [auth AAA] MOL2 format, chain W [auth AAA] MOL2 format, chain V [auth AAA] MOL2 format, chain U [auth AAA] MOL2 format, chain T [auth AAA] MOL2 format, chain S [auth AAA] MOL2 format, chain R [auth AAA] MOL2 format, chain Q [auth AAA] MOL2 format, chain P [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain EA [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain DA [auth AAA] MOL2 format, chain CA [auth AAA] MOL2 format, chain BA [auth AAA] mmCIF format, chain X [auth AAA] mmCIF format, chain W [auth AAA] mmCIF format, chain V [auth AAA] mmCIF format, chain U [auth AAA] mmCIF format, chain T [auth AAA] mmCIF format, chain S [auth AAA] mmCIF format, chain R [auth AAA] mmCIF format, chain Q [auth AAA] mmCIF format, chain P [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain EA [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain DA [auth AAA] mmCIF format, chain CA [auth AAA] mmCIF format, chain BA [auth AAA]	BA [auth AAA] CA [auth AAA] DA [auth AAA] E [auth AAA] EA [auth AAA] BA [auth AAA], CA [auth AAA], DA [auth AAA], E [auth AAA], EA [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], M [auth AAA], N [auth AAA], O [auth AAA], P [auth AAA], Q [auth AAA], R [auth AAA], S [auth AAA], T [auth AAA], U [auth AAA], V [auth AAA], W [auth AAA], X [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth AAA] Focus chain CA [auth AAA] Focus chain DA [auth AAA] Focus chain E [auth AAA] Focus chain EA [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain U [auth AAA] Focus chain V [auth AAA] Focus chain W [auth AAA] Focus chain X [auth AAA] Interactions & Density Focus chain BA [auth AAA] Focus chain CA [auth AAA] Focus chain DA [auth AAA] Focus chain E [auth AAA] Focus chain EA [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain U [auth AAA] Focus chain V [auth AAA] Focus chain W [auth AAA] Focus chain X [auth AAA]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain HA [auth AAA] SDF format, chain GA [auth AAA] MOL2 format, chain HA [auth AAA] MOL2 format, chain GA [auth AAA] mmCIF format, chain HA [auth AAA] mmCIF format, chain GA [auth AAA]	GA [auth AAA], HA [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain GA [auth AAA] Focus chain HA [auth AAA] Interactions & Density Focus chain GA [auth AAA] Focus chain HA [auth AAA]