8AX3 | pdb_00008ax3

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

PDB DOI: https://doi.org/10.2210/pdb8AX3/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: 1.59 Å
R-Value Free:
0.212 (Depositor), 0.196 (DCC)
R-Value Work:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 117.6 kDa
Atom Count: 9,262
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
Lysosomal acid 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: 3	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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 O [auth A] SDF format, chain VA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain VA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain VA [auth B]	O [auth A], VA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth A] Focus chain VA [auth B] Interactions & Density Focus chain O [auth A] Focus chain VA [auth B]
OD0 (Subject of Investigation/LOI) Query on OD0 Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain XA [auth B] SDF format, chain YA [auth B] SDF format, chain W [auth A] MOL2 format, chain T [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain W [auth A] mmCIF format, chain T [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain W [auth A]	T [auth A], W [auth A], XA [auth B], YA [auth B]	(1~{S},2~{R},3~{S},6~{S})-6-fluoranylcyclohex-4-ene-1,2,3-triol C₆ H₉ F O₃ DGGHLTXNAWHUTK-UNTFVMJOSA-N		Interactions Focus chain T [auth A] Focus chain W [auth A] Focus chain XA [auth B] Focus chain YA [auth B] Interactions & Density Focus chain T [auth A] Focus chain W [auth A] Focus chain XA [auth B] Focus chain YA [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain JA [auth B] SDF format, chain MA [auth B] SDF format, chain R [auth A] SDF format, chain WA [auth B] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain G [auth A]	F [auth A] G [auth A] JA [auth B] MA [auth B] R [auth A] F [auth A], G [auth A], JA [auth B], MA [auth B], R [auth A], WA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain MA [auth B] Focus chain R [auth A] Focus chain WA [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth B] Focus chain MA [auth B] Focus chain R [auth A] Focus chain WA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EB [auth B] MOL2 format, chain EB [auth B] mmCIF format, chain EB [auth B]	EB [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EB [auth B] Interactions & Density Focus chain EB [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain GA [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain I [auth A] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain JB [auth B] SDF format, chain K [auth A] SDF format, chain KB [auth B] SDF format, chain LA [auth B] SDF format, chain LB [auth B] SDF format, chain N [auth A] SDF format, chain NB [auth B] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain X [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain Y [auth A] SDF format, chain V [auth A] SDF format, chain RA [auth B] SDF format, chain NA [auth B] SDF format, chain MB [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain GB [auth B] SDF format, chain EA [auth A] SDF format, chain DB [auth B] SDF format, chain BB [auth B] SDF format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain V [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain V [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain MB [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain GB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], EA [auth A], FA [auth A], FB [auth B], GA [auth A], GB [auth B], H [auth A], HA [auth A], HB [auth B], I [auth A], IB [auth B], J [auth A], JB [auth B], K [auth A], KA [auth B], KB [auth B], L [auth A], LA [auth B], LB [auth B], M [auth A], MB [auth B], N [auth A], NA [auth B], NB [auth B], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], RA [auth B], S [auth A], SA [auth B], TA [auth B], U [auth A], UA [auth B], V [auth A], X [auth A], Y [auth A], Z [auth A], ZA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain OB [auth B] MOL2 format, chain OB [auth B] mmCIF format, chain OB [auth B]	OB [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain OB [auth B] Interactions & Density Focus chain OB [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain IA [auth A] MOL2 format, chain IA [auth A] mmCIF format, chain IA [auth A]	IA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain IA [auth A] Interactions & Density Focus chain IA [auth A]