Structure of PDB 6czd Chain D Binding Site BS01

Receptor Information

>6czd Chain D (length=227) Species: 83332 (Mycobacterium tuberculosis H37Rv)

HGGTILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDD
DLAEVGRLAGVTQLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADL
DRPGRLTLVEGAGGLLVELAEPGVTLRDVAVDVAAAALVVVTADLGTLNH
TKLTLEALAAQQVSCAGLVIGSWPDPPGLVAASNRSALARIAMVRAALPA
GAASLDAGDFAAMSAAAFDRNWVAGLV

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: 6czd Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6czd Precipitant-ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): T16 D49 E108
• Binding residue (residue number reindexed from 1): T18 D51 E110
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T11 G12 K15 T16 K37 T41 G54 E108
• Catalytic site (residue number reindexed from 1): T13 G14 K17 T18 K39 T43 G56 E110
• 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:6czd, PDBe:6czd, PDBj:6czd
• PDBsum: 6czd
• PubMed: 30289406
• UniProt: P9WPQ5|BIOD_MYCTU Dethiobiotin synthetase BioD (Gene Name=bioD)