Structure of PDB 3dyo Chain A Binding Site BS06

Receptor Information
>3dyo Chain A (length=1011) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAW
FPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVNPP
FVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYG
QDSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDV
SLLHKPTTQISDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQ
GETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPKLWSAEIPNLYRAV
VELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRHEHHPL
HGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLYVVDE
ANIETNGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNES
GHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDEDQPF
PAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQYPRL
QGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFADRT
PHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALDGKP
LASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWSEAG
HISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFNRQS
GFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVSEATRIDPNAWVERWKA
AGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRIDGSG
QMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPDRLTA
ACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNISRY
SQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAG
RYHYQLVWCQK
Ligand information
Ligand IDIPT
InChIInChI=1S/C9H18O5S/c1-4(2)15-9-8(13)7(12)6(11)5(3-10)14-9/h4-13H,3H2,1-2H3/t5-,6+,7+,8-,9+/m1/s1
InChIKeyBPHPUYQFMNQIOC-NXRLNHOXSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)S[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O
ACDLabs 10.04S(C(C)C)C1OC(C(O)C(O)C1O)CO
OpenEye OEToolkits 1.5.0CC(C)S[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O
OpenEye OEToolkits 1.5.0CC(C)SC1C(C(C(C(O1)CO)O)O)O
CACTVS 3.341CC(C)S[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
FormulaC9 H18 O5 S
Name1-methylethyl 1-thio-beta-D-galactopyranoside;
ISOPROPYL-1-BETA-D-THIOGALACTOSIDE;
1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE;
1-methylethyl 1-thio-beta-D-galactoside;
1-methylethyl 1-thio-D-galactoside;
1-methylethyl 1-thio-galactoside
ChEMBL
DrugBankDB01862
ZINCZINC000004261913
PDB chain3dyo Chain B Residue 2004 [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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PDB3dyo Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli).
Resolution1.8 Å
Binding residue
(original residue number in PDB)		D507 E508
Binding residue
(residue number reindexed from 1)		D495 E496
Annotation score1
Binding affinityMOAD: Ki=5mM
PDBbind-CN: -logKd/Ki=2.30,Ki=5.0mM
BindingDB: Ki=7.6e+4nM
Enzymatic activity
Catalytic site (original residue number in PDB) D201 H357 H391 E416 N418 E461 Y503 E537 N597 F601 N604
Catalytic site (residue number reindexed from 1) D189 H345 H379 E404 N406 E449 Y491 E525 N585 F589 N592
Enzyme Commision number 3.2.1.23: beta-galactosidase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004565 beta-galactosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
GO:0031420 alkali metal ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005990 lactose catabolic process
GO:0009056 catabolic process
Cellular Component
GO:0009341 beta-galactosidase complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dyo, PDBe:3dyo, PDBj:3dyo
PDBsum3dyo
PubMed19472413
UniProtP00722|BGAL_ECOLI Beta-galactosidase (Gene Name=lacZ)

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