Structure of PDB 3mle Chain D Binding Site BS03

Receptor Information
>3mle Chain D (length=223) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FQGHMLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAIN
HSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDT
DNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLIS
HDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNT
RSNNPIVIFQQSLKVLMSFALKG
Ligand information
Ligand ID8AC
InChIInChI=1S/C8H17NO2/c9-7-5-3-1-2-4-6-8(10)11/h1-7,9H2,(H,10,11)
InChIKeyUQXNEWQGGVUVQA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C(CCCC(=O)O)CCCN
CACTVS 3.370NCCCCCCCC(O)=O
ACDLabs 12.01O=C(O)CCCCCCCN
FormulaC8 H17 N O2
Name8-aminooctanoic acid;
8-aminocaprylic acid
ChEMBLCHEMBL196105
DrugBank
ZINCZINC000001689483
PDB chain3mle Chain D Residue 224 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3mle Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		G151 I153 N154
Binding residue
(residue number reindexed from 1)		G155 I157 N158
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) T9 N10 K13 T14 K35 T39 D50 E116
Catalytic site (residue number reindexed from 1) T13 N14 K17 T18 K39 T43 D54 E120
Enzyme Commision number 6.3.3.3: dethiobiotin synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004141 dethiobiotin synthase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0009102 biotin biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3mle, PDBe:3mle, PDBj:3mle
PDBsum3mle
PubMed22284390
UniProtO24872|BIOD_HELPY ATP-dependent dethiobiotin synthetase BioD (Gene Name=bioD)

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