Structure of PDB 5dl0 Chain A Binding Site BS01

Receptor Information
>5dl0 Chain A (length=924) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EHDWKKCDQSGFCRRNRAYADHALSAISWESPYKIAPETGSFKDGQYQAI
ILKTINDHGETVRLPLTVSFLESGTARVTIDEEKRQKGEIELRHDSKARK
ERYNEAEQWVIVGGMTLDKGAKVDYEDKTQMTVKYGPSSKFEATIKFAPF
SIDFKRDGASHIKFNDQGLLNIEHWRPKIDPPDDSTWWEESFGGNTDSKP
RGPESVGLDISFVGYEHVFGIPSHASPLSLKQTRGGEGNYNEPYRMYNAD
VFEYILDSPMTLYGSIPFMQAHRKDSSVGIFWLNAAETWVDITKGKDSKN
PLALGVKSKITTRTHWFSESGLLDVFVFLGPTPKDIISKYAELTGTTAMP
QEFSLGYHQCRWNYVSDEDVKDVDRKMDKFNMPYDVIWLDIEYTDEKKYF
TWDKHSFKDPIGMGKQLEAHGRKLVTIIDPHIKNTNNYPVVDELKSKDLA
VKTKDGSIFEGWCWPGSSHWIDAFNPAAREWWKGLFKYDKFKGTMENTFI
WNAMNEPSVFNGPEVTMPKDNLHHGNWEHRDVHNLNGMTFQNATYHALLS
RKPGEHRRPFVLTRAFFAGSQRLGAMWTGDNTADWGYLKASIPMVLSQGI
AGFPFAGADVGGFFGNPDKDLLTRWYQTGIFYPFFRAHAHIDARRREPYL
TGEPYNTIIAAALRLRYSLLPSWYTAFRHAHLDGTPIIKPMFYTHPSEEA
GLPIDDQFFIGNTGLLAKPVTDKDRTSVDIWIPDSEVYYDYFTYDIISAA
KSKTATLDAPLEKIPLLMRGGHVFARRDIPRRSSALMKWDPYTLVVVLGN
DRKAEGDLYVDDGDSFDYEKGQYIHRRFIFDANTLTSADYEGRDDASIKE
GEWLKKMRTVNVEKIIVVGAPAAWKGKKTVTVESEGKTWAAAIEYNPAEK
SRAAFAVVKKVGVRVGADFKIVFG
Ligand information
Ligand IDMAN
InChIInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6+/m1/s1
InChIKeyWQZGKKKJIJFFOK-PQMKYFCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O
ACDLabs 10.04OC1C(O)C(OC(O)C1O)CO
FormulaC6 H12 O6
Namealpha-D-mannopyranose;
alpha-D-mannose;
D-mannose;
mannose
ChEMBLCHEMBL365590
DrugBank
ZINCZINC000003860903
PDB chain5dl0 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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PDB5dl0 Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D303 F305 M557 D633
Binding residue
(residue number reindexed from 1)		D250 F252 M504 D580
Annotation score4
Enzymatic activity
Enzyme Commision number 3.2.1.20: alpha-glucosidase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
GO:0090599 alpha-glucosidase activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006491 N-glycan processing
Cellular Component
GO:0017177 glucosidase II complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dl0, PDBe:5dl0, PDBj:5dl0
PDBsum5dl0
PubMed26847925
UniProtG0SG42

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