Structure of PDB 3vd3 Chain D Binding Site BS01

Receptor Information
>3vd3 Chain D (length=1011) Species: 562 (Escherichia coli) [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
ANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGDES
GHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDEDQPF
PAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQYPRL
QGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFADRT
PHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALDGKP
LASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWSEAG
HISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFNRQS
GFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVSEATRIDPNAWVERWKA
AGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRIDGSG
QMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPDRLTA
ACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNISRY
SQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAG
RYHYQLVWCQK
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain3vd3 Chain D Residue 3001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vd3 Substitution for Asn460 cripples {beta}-galactosidase (Escherichia coli) by increasing substrate affinity and decreasing transition state stability.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		E416 H418 E461
Binding residue
(residue number reindexed from 1)		E404 H406 E449
Annotation score4
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
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Cellular Component
External links
PDB RCSB:3vd3, PDBe:3vd3, PDBj:3vd3
PDBsum3vd3
PubMed22446164
UniProtP00722|BGAL_ECOLI Beta-galactosidase (Gene Name=lacZ)

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