Structure of PDB 7pm4 Chain D Binding Site BS01

Receptor Information

>7pm4 Chain D (length=431) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

RYTPDWPSLDSRPLPAWFDEAKFGVFIHWGVFSVPAWGSEWFWWHWQGEG
RPQYQRFMRDNYPPGFSYADFGPQFTARFFHPEEWADLFQAAGAKYVVLT
TKHHEGFTNWPSPVSWNWNSKDVGPHRDLVGELGTALRKRNIRYGLYHSL
LEWFHPLYLLDKKNGFKTQHFVSAKTMPELYDLVNSYKPDLIWSDGEWEC
PDTYWNSTNFLSWLYNDSPVKDEVVVNDRWGQNCSCHHGGYYNCEDKFKP
QSLPDHKWEMCTSIDKFSWGYRRDMALSDVTEESEIISELVQTVSLGGNY
LLNIGPTKDGLIVPIFQERLLAVGKWLSINGEAIYASKPWRVQWEKNTTS
VWYTSKGSAVYAIFLHWPENGVLNLESPITTSTTKITMLGIQGDLKWSTD
PDKGLFISLPQLPPSAVPAEFAWTIKLTGVK

Ligand information

Ligand ID

DFU

InChI

InChI=1S/C6H13NO3/c1-3-5(9)6(10)4(8)2-7-3/h3-10H,2H2,1H3/t3-,4+,5+,6-/m0/s1

InChIKey

VYOCYWDJTQRZLC-KCDKBNATSA-N

SMILES

Software	SMILES
ACDLabs 10.04	OC1C(NCC(O)C1O)C
CACTVS 3.341	C[C@@H]1NC[C@@H](O)[C@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0	C[C@H]1[C@H]([C@H]([C@@H](CN1)O)O)O
OpenEye OEToolkits 1.5.0	CC1C(C(C(CN1)O)O)O
CACTVS 3.341	C[CH]1NC[CH](O)[CH](O)[CH]1O

Formula

C6 H13 N O3

Name

(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL;
DEOXYFUCONOJIRIMYCIN

PDB chain

7pm4 Chain D Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	7pm4 Cryo-EM structures of human fucosidase FucA1 reveal insight into substrate recognition and catalysis.
Resolution	2.49 Å
Binding residue (original residue number in PDB)	H58 E70 W71 H133 D225 D276 W299
Binding residue (residue number reindexed from 1)	H28 E40 W41 H103 D195 D246 W269
Annotation score	1

Enzymatic activity

Enzyme Commision number

3.2.1.51: alpha-L-fucosidase.

Gene Ontology

	Molecular Function
GO:0004560	alpha-L-fucosidase activity
GO:0005515	protein binding
GO:0015928	fucosidase activity
GO:0016798	hydrolase activity, acting on glycosyl bonds

	Biological Process
GO:0005975	carbohydrate metabolic process
GO:0006004	fucose metabolic process
GO:0006027	glycosaminoglycan catabolic process
GO:0006629	lipid metabolic process
GO:0016139	glycoside catabolic process
GO:0019377	glycolipid catabolic process

	Cellular Component
GO:0005576	extracellular region
GO:0005737	cytoplasm
GO:0005764	lysosome
GO:0035578	azurophil granule lumen
GO:0043202	lysosomal lumen
GO:0043231	intracellular membrane-bounded organelle
GO:0070062	extracellular exosome

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:7pm4, PDBe:7pm4, PDBj:7pm4
PDBsum	7pm4
PubMed	35907402
UniProt	P04066\|FUCO_HUMAN Tissue alpha-L-fucosidase (Gene Name=FUCA1)

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