Structure of PDB 3t0d Chain D Binding Site BS01

Receptor Information
>3t0d Chain D (length=1015) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEW
RFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPIT
VNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRW
VGYGQDSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGI
FRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTV
SLWQGETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPKLWSAEIPNL
YRAVVELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRHE
HHPLHGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLY
VVDEANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSL
GNESGHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDE
DQPFPAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQ
YPRLQGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVF
ADRTPHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVAL
DGKPLASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAW
SEAGHISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQF
NRQSGFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVTEATRIDPNAWVE
RWKAAGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRI
DGSGQMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPD
RLTAACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFN
ISRYSQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQ
LSAGRYHYQLVWCQK
Ligand information
Ligand ID149
InChIInChI=1S/C6H10O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-5,7-10H,1H2/t2-,3+,4+,5-/m1/s1
InChIKeyPHOQVHQSTUBQQK-MGCNEYSASA-N
SMILES
SoftwareSMILES
CACTVS 3.352OC[CH]1OC(=O)[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 1.7.0C([C@@H]1[C@@H]([C@@H]([C@H](C(=O)O1)O)O)O)O
ACDLabs 10.04O=C1OC(CO)C(O)C(O)C1O
OpenEye OEToolkits 1.7.0C(C1C(C(C(C(=O)O1)O)O)O)O
CACTVS 3.352OC[C@H]1OC(=O)[C@H](O)[C@@H](O)[C@H]1O
FormulaC6 H10 O6
NameD-galactonolactone;
(3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-one
ChEMBL
DrugBankDB01885
ZINCZINC000003881805
PDB chain3t0d Chain D 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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PDB3t0d Ser-796 of Beta-galactosidase (E. coli) plays a Key role in Maintaining an Optimum Balance between the Opened and Closed Conformations of the Catalytically Important Active Site Loop
Resolution1.93 Å
Binding residue
(original residue number in PDB)		D201 H391 N460 E461 M502 Y503 E537 H540 W568 F601 N604
Binding residue
(residue number reindexed from 1)		D193 H383 N452 E453 M494 Y495 E529 H532 W560 F593 N596
Annotation score4
Binding affinityMOAD: Ki=4.3mM
PDBbind-CN: -logKd/Ki=2.37,Ki=4.3mM
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) D193 H349 H383 E408 H410 E453 Y495 E529 N589 F593 N596
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:3t0d, PDBe:3t0d, PDBj:3t0d
PDBsum3t0d
PubMed22155115
UniProtP00722|BGAL_ECOLI Beta-galactosidase (Gene Name=lacZ)

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