Structure of PDB 5i0d Chain A Binding Site BS07

Receptor Information
>5i0d Chain A (length=1060) Species: 169963 (Listeria monocytogenes EGD-e) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDGEYHSPYGDDDLYTVQPTERSPRDPKAGEDVILNITTWPIENGQDVWV
EWTKNGVAQENVTAAYDYNSGNNTYWKADLGKFEKGDEITYTTKGSTNGG
TAYESGPFTFYVTDWEYVQDVTSVVDNGDSITLNMTATAGDFSPKLYLSF
EDLDTLRMELSPTGKETGHAGKSGYTVEDTAEKVTVTTEDLSIEIQKSPY
RMEVHQADGTLLTSEYTTANSLGWLTDGKNVINQYQNNFMTPSDEAFYGF
GERYDTINQRGKDVETYVYNEYQDQAQTERTYLAVPFFVSANKYGMYVNS
DFHSQFQMASKVEDKYSFVLDNDGDMTNMLDYYVISGKDQNDIVNNYTDI
TGKTTLLPKWAFGLWMSANEWDRESDVSSALSNAKANDIPATGFVLEQWS
DEETYYIWNNATYTAKKNGEAFSYDDFTFNGKWTDPKGMVDSVHDAGMNI
VLWQVPVLKDDGTVYEQRDNDEEYMISQGYSADDGTGAPYRVPASQWFGN
GILLDFTNKDAVDWWTSQREYLLTEVGIDGFKTDGGEMVWGRDTTFSNGE
KGQEMRNRYPTDYVSSYFDFAKSINPEAVSFSRSGTSGAQKSGIYWSGDQ
TSTFDSFQASLKAGLSASTSGVSYWAWDMAGFTGDYPTAELYKRATAMAA
FAPIMQFHSEKSDPSPSEERSPWNAVARTGDETILPTFQKYLYTRMNLLP
YIYTAAKDTADNGKSMMRQMAMDYPEDVNARDLDEQYMFGDDLLVAPIVQ
EGQTEKEVYLPEGEWVDIWNGGVHPGGETISYYADVDTLPVFAKAGAIIP
MNMTDGYQLGQNVGNDLKSYDNLTFRVYPSGDSEYSFYDDVNGGEMRDIS
VSEDFANEKVSVDLPAMADETTMQVFSTEPTSVTIDGADVAKADTLDAFN
EATTGYYYDTVQNLTYVKAAAKDAKQAIVLNGVNHAPYEAEFGHLTNVTT
ASDHAGYTGTGFVAGFDAEKEAVEFDIDAVDGASDYTMEVRYSAGVEDAT
RTVYINGKKQQITLPKTANWDTWNTVEVPVTLQAGNNQVVFDFEADDTAG
INFDHVVIKK
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 chain5i0d Chain F Residue 4 [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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PDB5i0d Transferase Versus Hydrolase: The Role of Conformational Flexibility in Reaction Specificity.
Resolution1.77 Å
Binding residue
(original residue number in PDB)		E428 D565 R614 W627 D630 H689
Binding residue
(residue number reindexed from 1)		E397 D534 R583 W596 D599 H658
Annotation score4
Enzymatic activity
Enzyme Commision number ?
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:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5i0d, PDBe:5i0d, PDBj:5i0d
PDBsum5i0d
PubMed28089449
UniProtQ8Y4J2

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