Structure of PDB 1dah Chain A Binding Site BS01

Receptor Information

>1dah Chain A (length=224) Species: 562 (Escherichia coli)

SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGL
RNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSA
GLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLG
CINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLL
GEIPWLAENPENAATGKYINLALL

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 1dah Chain A Residue 369

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1dah Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate.
• Resolution: 1.64 Å
• Binding residue (original residue number in PDB): T16 D54 E115
• Binding residue (residue number reindexed from 1): T16 D54 E115
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T11 E12 K15 T16 K37 S41 D54 E115
• Catalytic site (residue number reindexed from 1): T11 E12 K15 T16 K37 S41 D54 E115
• 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:0042803 protein homodimerization 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:1dah, PDBe:1dah, PDBj:1dah
• PDBsum: 1dah
• PubMed: 7669756
• UniProt: P13000|BIOD1_ECOLI ATP-dependent dethiobiotin synthetase BioD 1 (Gene Name=bioD1)