Structure of PDB 3vd9 Chain B Binding Site BS03

Receptor Information
>3vd9 Chain B (length=1016) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGE
WRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPI
TVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGR
WVGYGQDSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSG
IFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVT
VSLWQGETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPKLWSAEIPN
LYRAVVELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRH
EHHPLHGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGL
YVVDEANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWS
LGSESGHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVD
EDQPFPAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFR
QYPRLQGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLV
FADRTPHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVA
LDGKPLASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATA
WSEAGHISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQ
FNRQSGFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVSEATRIDPNAWV
ERWKAAGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYR
IDGSGQMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYP
DRLTAACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQF
NISRYSQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEF
QLSAGRYHYQLVWCQK
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 chain3vd9 Chain B Residue 2001 [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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PDB3vd9 Substitution for Asn460 cripples {beta}-galactosidase (Escherichia coli) by increasing substrate affinity and decreasing transition state stability.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		N102 D201 E461 E537 H540 N604 W999
Binding residue
(residue number reindexed from 1)		N95 D194 E454 E530 H533 N597 W992
Annotation score1
Binding affinityMOAD: Ki=0.1mM
BindingDB: Ki=7.6e+4nM
Enzymatic activity
Catalytic site (original residue number in PDB) D201 H357 H391 E416 H418 E461 Y503 E537 N597 F601 N604
Catalytic site (residue number reindexed from 1) D194 H350 H384 E409 H411 E454 Y496 E530 N590 F594 N597
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:3vd9, PDBe:3vd9, PDBj:3vd9
PDBsum3vd9
PubMed22446164
UniProtP00722|BGAL_ECOLI Beta-galactosidase (Gene Name=lacZ)

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