6Q6N: Recombinant human beta-glucocerebrosidase

Crystal structure of recombinant human beta-glucocerebrosidase in complex with biphenyl-cyclophellitol inhibitor (ME655). Determined by X-ray diffraction at 1.63 Å resolution. Released 27 Mar 2019.

Method: X-ray diffraction
Resolution: 1.63 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,125
Mol. weight: 116.12 kDa
Ligands: HK2, NAG
Released: 27 Mar 2019

Explore 6Q6N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q6N contains 49 α-helices and 55 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: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	6-7	2	2
β-strand	15-18	4	2
β-strand	25	1	1
α-helix	27-29	3
α-helix	32-33	2
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
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	335-341	7	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	445-450	6	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: 25 helices, 28 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	26-27	2
α-helix	29	1
α-helix	32-33	2
β-strand	36-43	8	8
β-strand	50-57	8	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	196	1	11
β-strand	197	1	10
α-helix	204-222	19
β-strand	229-231	3	9
α-helix	236-240	5
β-strand	250	1	11
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	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
Glucosylceramidase	A, B	protein	497	Homo sapiens	P04062 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6Q6N_1 Glucosylceramidase (chains A, B)
ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANH
TGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIR
VPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWT
SPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGL
LSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPE
AAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRG
MQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHL
GHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFL
ETISPGYSIHTYLWHRQ

Ligands and cofactors

ID	Name	Formula	Copies
HK2	(1~{S},3~{S},4~{R},6~{R})-2,3,4,6-tetrakis(oxidanyl)-5-[[4-[3-(4-phenylphenoxy)…	C24 H28 N3 O6	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (ACT, SO4) are not listed.

Primary citation

Functionalized Cyclophellitols Are Selective Glucocerebrosidase Inhibitors and Induce a Bona Fide Neuropathic Gaucher Model in Zebrafish. Artola, M., Kuo, C.L., Lelieveld, L.T. et al. J Am Chem Soc (2019) 141:4214-4218. DOI 10.1021/jacs.9b00056 · 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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