Structure of PDB 3mle Chain D Binding Site BS02

Receptor Information

>3mle Chain D (length=223) Species: 85962 (Helicobacter pylori 26695)

FQGHMLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAIN
HSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDT
DNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLIS
HDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNT
RSNNPIVIFQQSLKVLMSFALKG

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 3mle Chain D Residue 222

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3mle Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): T14 D50 E116
• Binding residue (residue number reindexed from 1): T18 D54 E120
• Annotation score: 1

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

External links

• PDB: RCSB:3mle, PDBe:3mle, PDBj:3mle
• PDBsum: 3mle
• PubMed: 22284390
• UniProt: O24872|BIOD_HELPY ATP-dependent dethiobiotin synthetase BioD (Gene Name=bioD)