Structure of PDB 2v3d Chain A

Receptor sequence
>2v3dA (length=495) Species: 9606 (Homo sapiens) [Search protein sequence]
EFARPCIPKSFGYSSVVCVCNATYCDSFDPALGTFSRYESTRSGRRMELS
MGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQN
LLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEE
DTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPG
DIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFT
PEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAA
KYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSV
RLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPI
IVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHP
DGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ
3D structure
PDB2v3d Crystal Structures of Complexes of N-Butyl- and N-Nonyl-Deoxynojirimycin Bound to Acid Beta-Glucosidase: Insights Into the Mechanism of Chemical Chaperone Action in Gaucher Disease.
ChainA
Resolution1.96 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) E235 E340 C342 N370
Catalytic site (residue number reindexed from 1) E233 E338 C340 N368
Enzyme Commision number 2.4.1.-
3.2.1.-
3.2.1.45: glucosylceramidase.
3.2.1.46: galactosylceramidase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 NBV A D127 F128 W179 N234 E235 F246 Y313 E340 W381 N396 D125 F126 W177 N232 E233 F244 Y311 E338 W379 N394 MOAD: Ki=116uM
PDBbind-CN: -logKd/Ki=3.94,Ki=116uM
BindingDB: IC50=400000nM,Ki=116000nM
Gene Ontology
Molecular Function
GO:0004336 galactosylceramidase activity
GO:0004348 glucosylceramidase activity
GO:0005102 signaling receptor binding
GO:0005124 scavenger receptor binding
GO:0005515 protein binding
GO:0008422 beta-glucosidase activity
GO:0016757 glycosyltransferase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0046527 glucosyltransferase activity
GO:0050295 steryl-beta-glucosidase activity
Biological Process
GO:0006665 sphingolipid metabolic process
GO:0006678 glucosylceramide metabolic process
GO:0006680 glucosylceramide catabolic process
GO:0006914 autophagy
GO:0007005 mitochondrion organization
GO:0007040 lysosome organization
GO:0007417 central nervous system development
GO:0008203 cholesterol metabolic process
GO:0008340 determination of adult lifespan
GO:0009267 cellular response to starvation
GO:0009268 response to pH
GO:0014004 microglia differentiation
GO:0016241 regulation of macroautophagy
GO:0019882 antigen processing and presentation
GO:0019915 lipid storage
GO:0021694 cerebellar Purkinje cell layer formation
GO:0021859 pyramidal neuron differentiation
GO:0022904 respiratory electron transport chain
GO:0023021 termination of signal transduction
GO:0030259 lipid glycosylation
GO:0031175 neuron projection development
GO:0031333 negative regulation of protein-containing complex assembly
GO:0032006 regulation of TOR signaling
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032715 negative regulation of interleukin-6 production
GO:0033077 T cell differentiation in thymus
GO:0033574 response to testosterone
GO:0042391 regulation of membrane potential
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043243 positive regulation of protein-containing complex disassembly
GO:0043407 negative regulation of MAP kinase activity
GO:0043524 negative regulation of neuron apoptotic process
GO:0043627 response to estrogen
GO:0046512 sphingosine biosynthetic process
GO:0046513 ceramide biosynthetic process
GO:0048469 cell maturation
GO:0048854 brain morphogenesis
GO:0048872 homeostasis of number of cells
GO:0050728 negative regulation of inflammatory response
GO:0050877 nervous system process
GO:0050905 neuromuscular process
GO:0051246 regulation of protein metabolic process
GO:0051248 negative regulation of protein metabolic process
GO:0051402 neuron apoptotic process
GO:0061436 establishment of skin barrier
GO:0061518 microglial cell proliferation
GO:0061744 motor behavior
GO:0071356 cellular response to tumor necrosis factor
GO:0071425 hematopoietic stem cell proliferation
GO:0071548 response to dexamethasone
GO:0072676 lymphocyte migration
GO:0097066 response to thyroid hormone
GO:0098773 skin epidermis development
GO:1901805 beta-glucoside catabolic process
GO:1903052 positive regulation of proteolysis involved in protein catabolic process
GO:1903061 positive regulation of protein lipidation
GO:1904457 positive regulation of neuronal action potential
GO:1905037 autophagosome organization
GO:1905165 regulation of lysosomal protein catabolic process
Cellular Component
GO:0005615 extracellular space
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0016020 membrane
GO:0043202 lysosomal lumen
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:2v3d, PDBe:2v3d, PDBj:2v3d
PDBsum2v3d
PubMed17666401
UniProtP04062|GBA1_HUMAN Lysosomal acid glucosylceramidase (Gene Name=GBA1)

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