Structure of PDB 3mle Chain A Binding Site BS03

Receptor Information
>3mle Chain A (length=221) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GHMLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHS
SDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDTDN
LTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLISHD
NLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRS
NNPIVIFQQSLKVLMSFALKG
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3mle Chain A Residue 226 [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)		N10 A11 G12 K13 T14 T15 N175
Binding residue
(residue number reindexed from 1)		N12 A13 G14 K15 T16 T17 N177
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=5.24,Kd=5.8uM
Enzymatic activity
Catalytic site (original residue number in PDB) T9 N10 K13 T14 K35 T39 D50 E116
Catalytic site (residue number reindexed from 1) T11 N12 K15 T16 K37 T41 D52 E118
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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