Structure of PDB 3t0b Chain A Binding Site BS03

Receptor Information

>3t0b Chain A (length=1014) Species: 83333 (Escherichia coli K-12)

VLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWR
FAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITV
NPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWV
GYGQDSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIF
RDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVS
LWQGETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPKLWSAEIPNLY
RAVVELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRHEH
HPLHGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLYV
VDEANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLG
NESGHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDED
QPFPAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQY
PRLQGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFA
DRTPHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALD
GKPLASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWS
EAGHISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFN
RQSGFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVTEATRIDPNAWVER
WKAAGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRID
GSGQMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPDR
LTAACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNI
SRYSQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQL
SAGRYHYQLVWCQK

Ligand information

• Ligand ID: IPT
• InChI: InChI=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
• InChIKey: BPHPUYQFMNQIOC-NXRLNHOXSA-N
• SMILES:
  CACTVS 3.341: CC(C)S[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: S(C(C)C)C1OC(C(O)C(O)C1O)CO
  OpenEye OEToolkits 1.5.0: CC(C)S[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)O
  OpenEye OEToolkits 1.5.0: CC(C)SC1C(C(C(C(O1)CO)O)O)O
  CACTVS 3.341: CC(C)S[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
• Formula: C9 H18 O5 S
• Name: 1-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
• DrugBank: DB01862
• ZINC: ZINC000004261913
• PDB chain: 3t0b Chain A Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3t0b er-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
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): N102 D201 E461 E537 H540 N604 W999
• Binding residue (residue number reindexed from 1): N93 D192 E452 E528 H531 N595 W990
• Annotation score: 1
• Binding affinity: MOAD: Ki=0.05mM
  PDBbind-CN: -logKd/Ki=4.30,Ki=0.05mM
  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): D192 H348 H382 E407 H409 E452 Y494 E528 N588 F592 N595
• 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

External links

• PDB: RCSB:3t0b, PDBe:3t0b, PDBj:3t0b
• PDBsum: 3t0b
• PubMed: 22155115
• UniProt: P00722|BGAL_ECOLI Beta-galactosidase (Gene Name=lacZ)