Structure of PDB 4zyr Chain A Binding Site BS01

Receptor Information
>4zyr Chain A (length=387) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTWIIFAAISLF
SLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILV
GSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCA
SIVGIMFTINNQFVFWLGSGCALILAVLLFFAKTDAFSLKLALELFRQPK
LWFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFWYVTTMGELL
NASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTL
HMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGN
MYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSL
Ligand information
Ligand ID9PG
InChIInChI=1S/C12H15NO8/c14-5-8-9(15)10(16)11(17)12(21-8)20-7-3-1-6(2-4-7)13(18)19/h1-4,8-12,14-17H,5H2/t8-,9+,10+,11-,12+/m1/s1
InChIKeyIFBHRQDFSNCLOZ-IIRVCBMXSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(C1OC(C(C(C1O)O)O)Oc2ccc([N+]([O-])=O)cc2)O
OpenEye OEToolkits 1.9.2c1cc(ccc1[N+](=O)[O-])O[C@@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O)O
OpenEye OEToolkits 1.9.2c1cc(ccc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O)O
CACTVS 3.385OC[CH]1O[CH](Oc2ccc(cc2)[N+]([O-])=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.385OC[C@H]1O[C@H](Oc2ccc(cc2)[N+]([O-])=O)[C@H](O)[C@@H](O)[C@H]1O
FormulaC12 H15 N O8
Name4-nitrophenyl alpha-D-galactopyranoside;
4-nitrophenyl alpha-D-galactoside;
4-nitrophenyl D-galactoside;
4-nitrophenyl galactoside
ChEMBLCHEMBL471489
DrugBank
ZINCZINC000004282287
PDB chain4zyr Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4zyr Structure of LacY with an alpha-substituted galactoside: Connecting the binding site to the protonation site.
Resolution3.312 Å
Binding residue
(original residue number in PDB)		M23 R144 C148 W151 E269 H322
Binding residue
(residue number reindexed from 1)		M18 R139 C143 W146 E248 H301
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.70,Kd~2uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005351 carbohydrate:proton symporter activity
GO:0005515 protein binding
GO:0015293 symporter activity
GO:0015528 lactose:proton symporter activity
GO:0022857 transmembrane transporter activity
GO:0030395 lactose binding
Biological Process
GO:0008643 carbohydrate transport
GO:0015767 lactose transport
GO:0034219 carbohydrate transmembrane transport
GO:0055085 transmembrane transport
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

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Biological Process
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Cellular Component
External links
PDB RCSB:4zyr, PDBe:4zyr, PDBj:4zyr
PDBsum4zyr
PubMed26157133
UniProtP02920|LACY_ECOLI Lactose permease (Gene Name=lacY)

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