Structure of PDB 4ayq Chain A Binding Site BS01

Receptor Information
>4ayq Chain A (length=434) Species: 366602 (Caulobacter sp. K31) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPEDWKALAADVRSEFQWAWQGYVAKAWGKDEINPVSGTSRSFFIEGHDL
GLSLVEALDTLWIMGLDAEFQAGVDWVKANLSFDVDGNAQVFETNIRLVG
GLLSAHLASGDPVLLAKARDLADRLAKAFEASPHGLPWRYVNLRTGAVSD
PETNLAEIGTYLSEFGVLSQLTGERKYFDMAKRAMRHTLDRRSKIGLMAA
NIHAMTGAFTSRNASIDVYADSFYEYLWDAWALFGDEDCKRWAVECVDAQ
LAHQAKRYDGRLWFPMVDFETGAVTGTAQSELAAYYAGLLGQVGRKAQGD
DYLASFTYLQATFGVIPESIDVTTGQPRRKHTGLRPEYPDACLNLWLIDR
DPRYRRLAAIHYREMKATSRAAFGYTALKDITTRPMTQDDNCPGYWWSEQ
MKYYYLLFSDTPRIDYGQLQLSTEANVLRGFRKV
Ligand information
Ligand IDMVL
InChIInChI=1S/C8H12N2O4/c11-3-4-5(12)6(13)7(14)8-9-1-2-10(4)8/h1-2,4-7,11-14H,3H2/t4-,5-,6+,7+/m1/s1
InChIKeyRZRDQZQPTISYKY-JWXFUTCRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cn2c(n1)C(C(C(C2CO)O)O)O
OpenEye OEToolkits 1.7.6c1cn2c(n1)[C@H]([C@H]([C@@H]([C@H]2CO)O)O)O
CACTVS 3.385OC[C@@H]1[C@@H](O)[C@H](O)[C@H](O)c2nccn12
ACDLabs 12.01n1ccn2c1C(O)C(O)C(O)C2CO
CACTVS 3.385OC[CH]1[CH](O)[CH](O)[CH](O)c2nccn12
FormulaC8 H12 N2 O4
Name(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL;
Mannoimidazole
ChEMBLCHEMBL1213397
DrugBank
ZINCZINC000003821680
PDB chain4ayq Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ayq 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)
D249 L310 R363 P364 E365 Y423 E427 T451 E452
Binding residue
(residue number reindexed from 1)
D221 L282 R335 P336 E337 Y395 E399 T423 E424
Annotation score1
Binding affinityMOAD: Kd=47nM
PDBbind-CN: -logKd/Ki=7.33,Kd=47nM
Enzymatic activity
Catalytic site (original residue number in PDB) E121 R125 D249 E365
Catalytic site (residue number reindexed from 1) E93 R97 D221 E337
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:4ayq, PDBe:4ayq, PDBj:4ayq
PDBsum4ayq
PubMed23012075
UniProtB0SWV2

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