Structure of PDB 3i3b Chain B Binding Site BS01

Receptor Information
>3i3b Chain B (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
ANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNES
GHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDEDQPF
PAVPKWSIKKWLSLPGETRPLILCEYAHAAGNSLGGFAKYWQAFRQYPRL
QGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFADRT
PHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALDGKP
LASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWSEAG
HISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFNRQS
GFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVSEATRIDPNAWVERWKA
AGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRIDGSG
QMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPDRLTA
ACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNISRY
SQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAG
RYHYQLVWCQK
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 chain3i3b 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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PDB3i3b Role of Met-542 as a guide for the conformational changes of Phe-601 that occur during the reaction of β-galactosidase (Escherichia coli).
Resolution2.2 Å
Binding residue
(original residue number in PDB)		D201 H391 E461 Y503 E537 H540 W568 F601 N604
Binding residue
(residue number reindexed from 1)		D189 H379 E449 Y491 E525 H528 W556 F589 N592
Annotation score4
Binding affinityMOAD: Ki=5.9mM
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) D189 H345 H379 E404 H406 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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3i3b, PDBe:3i3b, PDBj:3i3b
PDBsum3i3b
PubMed20921997
UniProtP00722|BGAL_ECOLI Beta-galactosidase (Gene Name=lacZ)

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