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Structure of PDB 1dah Chain A Binding Site BS03

Receptor Information

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

SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGL
RNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSA
GLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLG
CINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLL
GEIPWLAENPENAATGKYINLALL

Ligand information

• Ligand ID: ACP
• InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
• InChIKey: UFZTZBNSLXELAL-IOSLPCCCSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C11 H18 N5 O12 P3
• Name: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
  ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
• ChEMBL: CHEMBL133463
• DrugBank: DB03909
• ZINC: ZINC000008295124
• PDB chain: 1dah Chain A Residue 226

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): T11 E12 G14 K15 T16 V17 N175 W205 L206 P210
• Binding residue (residue number reindexed from 1): T11 E12 G14 K15 T16 V17 N175 W205 L206 P210
• Annotation score: 3

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)

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