Structure of PDB 3n8d Chain B Binding Site BS01

Receptor Information
>3n8d Chain B (length=334) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRK
QNNITAEIKSTDELHLEEISQLLKESSSGQPYDAVFPLLNGEDGTIQGLF
EVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYE
HNILKLVNDKLNYPVFVKPANLVGISKCNNEAELKEGIKEAFQFDRKLVI
EQGVNAREIEVAVLGNDYPEATWPGEVVKDVAFQLKIPADLDEDVQLTLR
NMALEAFKETDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWE
NMGLSYPELITKLIELAKERHQDKQKNKYKIDLE
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain3n8d 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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PDB3n8d Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F175 K177 I187 E213 G215 V216 E220 E306
Binding residue
(residue number reindexed from 1)		F166 K168 I175 E201 G203 V204 E208 E282
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E16 V19 L22 R291 D293 E306 N308 G312 F316
Catalytic site (residue number reindexed from 1) E15 V18 L21 R267 D269 E282 N284 G288 F292
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
View graph for
Cellular Component
External links
PDB RCSB:3n8d, PDBe:3n8d, PDBj:3n8d
PDBsum3n8d
PubMed20729361
UniProtQ5HEB7|DDL_STAAC D-alanine--D-alanine ligase (Gene Name=ddl)

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