Structure of PDB 5dkz Chain A Binding Site BS01

Receptor Information
>5dkz Chain A (length=921) 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
DRKAEGDLYVDDGDSFDYEKGQYIHRRFIFDANTLTSADYEGRDDKEGEW
LKKMRTVNVEKIIVVGAPAAWKGKKTVTVESEGKTWAAAIEYNPAEKSRA
AFAVVKKVGVRVGADFKIVFG
Ligand information
Ligand IDGLC
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-DVKNGEFBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@H]([C@H](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
ACDLabs 10.04OC1C(O)C(OC(O)C1O)CO
FormulaC6 H12 O6
Namealpha-D-glucopyranose;
alpha-D-glucose;
D-glucose;
glucose
ChEMBLCHEMBL423707
DrugBank
ZINCZINC000003861213
PDB chain5dkz 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5dkz Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D303 W415 M557 D633 F666
Binding residue
(residue number reindexed from 1)		D250 W362 M504 D580 F613
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dkz, PDBe:5dkz, PDBj:5dkz
PDBsum5dkz
PubMed26847925
UniProtG0SG42

[Back to BioLiP]