Structure of PDB 4ayr Chain A Binding Site BS02

Receptor Information
>4ayr Chain A (length=432) Species: 366602 (Caulobacter sp. K31) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDWKALAADVRSEFQWAWQGYVAKAWGKDEINPVSGTSRSFFIEGHDLGL
SLVEALDTLWIMGLDAEFQAGVDWVKANLSFDVDGNAQVFETNIRLVGGL
LSAHLASGDPVLLAKARDLADRLAKAFEASPHGLPWRYVNLRTGAVSDPE
TNLAEIGTYLSEFGVLSQLTGERKYFDMAKRAMRHTLDRRSKIGLMAANI
HAMTGAFTSRNASIDVYADSFYEYLWDAWALFGDEDCKRWAVECVDAQLA
HQAKRYDGRLWFPMVDFETGAVTGTAQSELAAYYAGLLGQVGRKAQGDDY
LASFTYLQATFGVIPESIDVTTGQPRRKHTGLRPEYPDACLNLWLIDRDP
RYRRLAAIHYREMKATSRAAFGYTALKDITTRPMTQDDNCPGYWWSEQMK
YYYLLFSDTPRIDYGQLQLSTEANVLRGFRKV
Ligand information
Ligand IDIFL
InChIInChI=1S/C6H11NO4/c8-2-3-1-7-6(11)5(10)4(3)9/h3-5,8-10H,1-2H2,(H,7,11)/t3-,4-,5+/m1/s1
InChIKeyARBXEMIAJIJEQI-WDCZJNDASA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NCC(CO)C(O)C1O
OpenEye OEToolkits 1.5.0C1C(C(C(C(=O)N1)O)O)CO
CACTVS 3.341OC[CH]1CNC(=O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1CNC(=O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H]([C@@H](C(=O)N1)O)O)CO
FormulaC6 H11 N O4
Name(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE;
ISOFAGOMINE LACTAM
ChEMBLCHEMBL1213445
DrugBank
ZINC
PDB chain4ayr Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ayr The Reaction Coordinate of a Bacterial Gh47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach.
Resolution1.1 Å
Binding residue
(original residue number in PDB)
F120 E185 Y247 D249
Binding residue
(residue number reindexed from 1)
F90 E155 Y217 D219
Annotation score1
Binding affinityMOAD: Kd=99nM
PDBbind-CN: -logKd/Ki=7.00,Kd=99nM
Enzymatic activity
Catalytic site (original residue number in PDB) E121 R125 D249 E365
Catalytic site (residue number reindexed from 1) E91 R95 D219 E335
Enzyme Commision number 3.2.1.113: mannosyl-oligosaccharide 1,2-alpha-mannosidase.
Gene Ontology
Molecular Function
GO:0004559 alpha-mannosidase activity
GO:0004571 mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
GO:0005509 calcium ion binding
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:1904382 mannose trimming involved in glycoprotein ERAD pathway
Cellular Component
GO:0016020 membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4ayr, PDBe:4ayr, PDBj:4ayr
PDBsum4ayr
PubMed23012075
UniProtB0SWV2

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