8AX3: Recombinant human beta-glucocerebrosidase

Name: PDB 8AX3: Structure of recombinant human beta-glucocerebrosidase in complex with L-carbaxylosyl fluoride
Published: 2024-03-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Structure of recombinant human beta-glucocerebrosidase in complex with L-carbaxylosyl fluoride. Determined by X-ray diffraction at 1.59 Å resolution. Released 13 Mar 2024.

Method: X-ray diffraction
Resolution: 1.59 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,262
Mol. weight: 117.6 kDa
Ligands: OD0, CA, NAG
Released: 13 Mar 2024

Explore 8AX3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AX3 contains 51 α-helices and 54 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: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	6-7	2	2
α-helix	14	1
β-strand	15-18	4	2
β-strand	25	1	1
α-helix	27-29	3
β-strand	36-43	8	3
β-strand	50-55	6	3
β-strand	57	1	3
β-strand	65-77	13	3
α-helix	78	1
β-strand	80-84	5	4
α-helix	87-94	8
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	197	1	5
α-helix	204-222	19
β-strand	229-231	3	4
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	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: 26 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	6
β-strand	6-8	3	7
β-strand	14-18	5	7
β-strand	25	1	6
α-helix	27-29	3
α-helix	32-33	2
β-strand	36-43	8	8
β-strand	50-55	6	8
α-helix	56	1
β-strand	57	1	8
β-strand	65-77	13	8
α-helix	78	1
β-strand	80-84	5	9
α-helix	87-94	8
α-helix	98-109	12
β-strand	118-123	6	9
α-helix	151	1
α-helix	152-157	6
α-helix	158-167	10
α-helix	171-172	2
β-strand	173-178	6	9
α-helix	183-185	3
β-strand	186	1	10
β-strand	197	1	10
α-helix	204-222	19
β-strand	229-231	3	9
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	9
α-helix	285-287	3
α-helix	290-296	7
α-helix	299-302	4
β-strand	307-311	5	9
α-helix	315-317	3
α-helix	320	1
α-helix	321-325	5
α-helix	326-330	5
β-strand	335-340	6	9
α-helix	357-372	16
β-strand	375-382	8	9
β-strand	385	1	7
β-strand	402-405	4	7
α-helix	406-408	3
β-strand	410-413	4	7
α-helix	415-424	10
β-strand	432-438	7	8
β-strand	444-450	7	8
β-strand	456-462	7	8
β-strand	468-474	7	8
β-strand	478-484	7	8
β-strand	488-494	7	8

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>8AX3_1 Lysosomal acid glucosylceramidase (chains A, B)
ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANH
TGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIR
VPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWT
SPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGL
LSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPE
AAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRG
MQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHL
GHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFL
ETISPGYSIHTYLWRRQ

Ligands and cofactors

ID	Name	Formula	Copies
OD0	(1~{S},2~{R},3~{S},6~{S})-6-fluoranylcyclohex-4-ene-1,2,3-triol	C6 H9 F O3	4
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (SO4, EDO, GOL, NA) are not listed.

Primary citation

Single turnover covalent inhibitors for functional chaperoning of lysosomal glycoside hydrolases. Bhosale, S., Kandalkar, S., Gilormini, P.A. et al. To be published.

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

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