Structure of PDB 1yqn Chain A Binding Site BS01

Receptor Information
>1yqn Chain A (length=158) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDAL
LGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTI
IAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGMGLGIAC
EAVALLIK
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain1yqn Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1yqn A double mutation of Escherichia coli2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate.
Resolution3.11 Å
Binding residue
(original residue number in PDB)		D8 H10 H42
Binding residue
(residue number reindexed from 1)		D10 H12 H44
Annotation score1
Enzymatic activity
Enzyme Commision number 4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
GO:0016829 lyase activity
GO:0030145 manganese ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006744 ubiquinone biosynthetic process
GO:0008299 isoprenoid biosynthetic process
GO:0016114 terpenoid biosynthetic process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1yqn, PDBe:1yqn, PDBj:1yqn
PDBsum1yqn
PubMed16511114
UniProtP62617|ISPF_ECOLI 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

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