Structure of PDB 2i8c Chain B Binding Site BS01

Receptor Information
>2i8c Chain B (length=347) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQ
NNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGED
GTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLR
SEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKE
AFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAFVQLQIPA
DLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGF
TAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKIDRSHH
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 chain2i8c Chain B Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2i8c Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies.
Resolution2.46 Å
Binding residue
(original residue number in PDB)		F175 K177 S183 G215 V216 E220 F295 N305 E306
Binding residue
(residue number reindexed from 1)		F173 K175 S181 G213 V214 E218 F282 N292 E293
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E16 V19 L22 H96 S183 R291 D293 E306 N308 G312 F316
Catalytic site (residue number reindexed from 1) E14 V17 L20 H94 S181 R278 D280 E293 N295 G299 F303
Enzyme Commision number 6.3.2.4: D-alanine--D-alanine ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0008716 D-alanine-D-alanine ligase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization
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:2i8c, PDBe:2i8c, PDBj:2i8c
PDBsum2i8c
PubMed17015835
UniProtQ5HEB7|DDL_STAAC D-alanine--D-alanine ligase (Gene Name=ddl)

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