Structure of PDB 3bvv Chain A Binding Site BS01

Receptor Information
>3bvv Chain A (length=1016) Species: 7227 (Drosophila melanogaster) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHH
KLKVFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWA
EISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVL
LQLTEGQTWLKQFMNVTPTASWAIAPFGHSPTMPYILQKSGFKNMLIQRT
HYSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDP
KVCCQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQWKKKAELY
RTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEHINSQAHFNVQAQFGTL
QEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRPYHKRMD
RVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAK
THVVVDYEQRMQEALKACQMVMQQSVYRLLTKPSIYSPDFSFSYFTLDDS
RWPGSGVEDSRTTIILGEDILPSKHVVMHNTLPHWREQLVDFYVSSPFVS
VTDLANNPVEAQVSPVWSWHHDTLTKTIHPQGSTTKYRIIFKARVPPMGL
ATYVLTISDSKPEHTSYASNLLLRKNPTSLPLGQYPEDVKFGDPREISLR
VGNGPTLAFSEQGLLKSIQLTQDSPHVPVHFKFLKYGVRSHGDRSGAYLF
LPNGPASPVELGQPVVLVTKGKLESSVSVGLPSVVHQTIMRGGAPEIRNL
VDIGSLDNTEIVMRLETHIDSGDIFYTDLNGLQFIKRRRLDKLPLQANYY
PIPSGMFIEDANTRLTLLTGQPLGGSSLASGELEIMQDRRLASDDERGLG
QGVLDNKPVLHIYRLVLEKVNNCVRPSKLHPAGYLTSAAHKASQSLLDPL
DKFIFAENEWIGAQGQFGGDHPSAREDLDVSVMRRLTKSSAKTQRVGYVL
HRTNLMQCGTPEEHTQKLDVCHLLPNVARCERTTLTFLQNLEHLDGMVAP
EVCPMETAAYVSSHSS
Ligand information
Ligand IDYZ0
InChIInChI=1S/C7H14O6/c1-12-7-6(11)5(10)4(9)3(2-8)13-7/h3-11H,2H2,1H3/t3-,4-,5+,6+,7-/m1/s1
InChIKeyHOVAGTYPODGVJG-ULQPCXBYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O
ACDLabs 12.01OC1C(O)C(O)C(OC1OC)CO
CACTVS 3.370CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 1.7.6COC1C(C(C(C(O1)CO)O)O)O
OpenEye OEToolkits 1.7.6CO[C@H]1[C@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
FormulaC7 H14 O6
Namemethyl beta-D-mannopyranoside
ChEMBLCHEMBL4117365
DrugBank
ZINCZINC000005998341
PDB chain3bvv Chain B Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3bvv Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		W95 D341 R876
Binding residue
(residue number reindexed from 1)		W66 D312 R847
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H90 D92 A204 D341 H471
Catalytic site (residue number reindexed from 1) H61 D63 A175 D312 H442
Enzyme Commision number 3.2.1.114: mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004559 alpha-mannosidase activity
GO:0004572 mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity
GO:0015923 mannosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006013 mannose metabolic process
GO:0006486 protein glycosylation
GO:0006491 N-glycan processing
GO:0016063 rhodopsin biosynthetic process
GO:0035010 encapsulation of foreign target
Cellular Component
GO:0000139 Golgi membrane
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3bvv, PDBe:3bvv, PDBj:3bvv
PDBsum3bvv
PubMed18558690
UniProtQ24451|MAN2_DROME Alpha-mannosidase 2 (Gene Name=alpha-Man-IIa)

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