8P3E: Glucocerebrosidase

Crystal structure of glucocerebrosidase in complex with allosteric activator. Determined by X-ray diffraction at 1.75 Å resolution. Released 6 Mar 2024.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,397
Mol. weight: 112.58 kDa
Ligands: WSI, NAG
Released: 6 Mar 2024

Explore 8P3E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P3E contains 49 α-helices and 56 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 26 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	6-8	3	2
β-strand	14-19	6	2
β-strand	25	1	1
α-helix	26-27	2
α-helix	29	1
α-helix	32-33	2
β-strand	36-43	8	3
β-strand	50-57	8	3
β-strand	65-77	13	3
α-helix	78	1
β-strand	80-84	5	4
α-helix	87-95	9
α-helix	98-109	12
β-strand	118-123	6	4
α-helix	151	1
α-helix	152-157	6
α-helix	158-167	10
α-helix	171-172	2
β-strand	173-178	6	4
α-helix	183-185	3
β-strand	186	1	5
β-strand	196	1	6
β-strand	197	1	5
α-helix	204-222	19
β-strand	229-231	3	4
α-helix	238-240	3
β-strand	250	1	6
α-helix	253-259	7
α-helix	260-264	5
α-helix	265-269	5
β-strand	277-284	8	4
α-helix	285-287	3
α-helix	290-296	7
α-helix	299-302	4
β-strand	307-311	5	4
α-helix	315-317	3
α-helix	320	1
α-helix	321-325	5
α-helix	326-330	5
β-strand	335-340	6	4
α-helix	357-372	16
β-strand	375-382	8	4
β-strand	385	1	2
β-strand	402-405	4	2
α-helix	406-408	3
β-strand	410-413	4	2
α-helix	415-424	10
β-strand	432-438	7	3
β-strand	444-450	7	3
β-strand	456-462	7	3
β-strand	468-474	7	3
β-strand	478-484	7	3
β-strand	488-494	7	3

Chain B: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	7
β-strand	6-8	3	8
β-strand	14-18	5	8
β-strand	25	1	7
α-helix	27-29	3
β-strand	36-42	7	9
β-strand	50-57	8	9
β-strand	65-77	13	9
α-helix	78	1
β-strand	80-84	5	10
α-helix	87-94	8
α-helix	98-109	12
β-strand	118-123	6	10
α-helix	151	1
α-helix	152-157	6
α-helix	158-167	10
α-helix	171-172	2
β-strand	173-178	6	10
α-helix	183-185	3
β-strand	186	1	11
β-strand	197	1	11
α-helix	204-222	19
β-strand	229-231	3	10
α-helix	236-240	5
α-helix	253-259	7
α-helix	260-264	5
α-helix	265-269	5
β-strand	277-284	8	10
α-helix	285-287	3
α-helix	290-296	7
α-helix	299-302	4
β-strand	307-313	7	10
α-helix	320	1
α-helix	321-325	5
α-helix	326-330	5
β-strand	335-342	8	10
β-strand	344	1	12
α-helix	357-372	16
β-strand	375-382	8	10
β-strand	385	1	8
β-strand	398	1	12
β-strand	402-405	4	8
α-helix	406-408	3
β-strand	410-413	4	8
α-helix	415-424	10
β-strand	432-438	7	9
β-strand	444-450	7	9
β-strand	456-462	7	9
β-strand	468-474	7	9
β-strand	478-484	7	9
β-strand	489-494	6	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glucosylceramidase	A, B	protein	497	Homo sapiens	P04062 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8P3E_1 Glucosylceramidase (chains A, B)
ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANH
TGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIR
VPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWT
SPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGL
LSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPE
AAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRG
MQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHL
GHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFL
ETISPGYSIHTYLWHRQ

Ligands and cofactors

ID	Name	Formula	Copies
WSI	2-[[3-[(4-chlorophenyl)carbamoyl]phenyl]sulfonylamino]benzoic acid	C20 H15 Cl N2 O5 S	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Identification of ss-Glucocerebrosidase Activators for Glucosylceramide hydrolysis. Schulze, M.E.D., Scholz, D., Jnoff, E. et al. ChemMedChem (2024) 19:e202300548-e202300548. DOI 10.1002/cmdc.202300548 · PubMed

Other PDB entries of the same protein (UniProt P04062 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TN1 0.98 Å, Unliganded Crystal Structure of Recombinant GBA
9FB2 1.14 Å, Gcase in complex with small molecule inhibitor 1
9FA3 1.36 Å, Gcase in complex with small molecule inhibitor 1
9FAL 1.39 Å, Gcase in complex with small molecule inhibitor 1
9FAY 1.4 Å, Gcase in complex with small molecule inhibitor 1
6TJQ 1.41 Å, Crystal Structure of Recombinant GBA in Complex with 2-Deoxy-2-fluoro-beta-D-glucopyranos…
9FDI 1.41 Å, Gcase in complex with small molecule inhibitor 1
8AWR 1.49 Å, Structure of recombinant human beta-glucocerebrosidase in complex with L-carbaxylosyl…
9FA6 1.49 Å, Gcase in complex with small molecule inhibitor 1
6TJK 1.56 Å, Crystal Structure of Recombinant GBA in Complex with Bis-Tris Propane.
8AWK 1.58 Å, Structure of recombinant human beta-glucocerebrosidase in complex with D-carbaxylosyl…
6TJJ 1.59 Å, Structure of Cerezyme at pH 4.6

Browse structure collections

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