Structure of PDB 3r5x Chain D Binding Site BS02

Receptor Information
>3r5x Chain D (length=306) Species: 1392 (Bacillus anthracis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NAMRIGVIMGGVSSEKQVSIMTGNEMIANLDKNKYEIVPITLNEKMDLIE
KAKDIDFALLALHGKYGEDGTVQGTLESLGIPYSGSNMLSSGICMDKNIS
KKILRYEGIETPDWIELTKMEDLNFDELDKLGFPLVVKPNSGGSSVGVKI
VYDKDELISMLETVFEWDSEVVIEKYIKGEEITCSIFDGKQLPIISIRHA
AEFFDYNAKYDDASTIEEVIELPAELKERVNKASLACYKALKCSVYARVD
MMVKDGIPYVMEVNTLPGMTQASLLPKSADAAGIHYSKLLDMIIETSLRV
RKEEGF
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain3r5x Chain D Residue 402 [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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PDB3r5x Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP
Resolution2.0 Å
Binding residue
(original residue number in PDB)		V134 K136 V146 E172 Y174 I175 E179 M250 M259 E260 N262
Binding residue
(residue number reindexed from 1)		V136 K138 V148 E174 Y176 I177 E181 M252 M261 E262 N264
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E13 V16 M19 H61 S142 N205 Y208 R246 D248 E260 N262 G266 A270
Catalytic site (residue number reindexed from 1) E15 V18 M21 H63 S144 N207 Y210 R248 D250 E262 N264 G268 A272
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3r5x, PDBe:3r5x, PDBj:3r5x
PDBsum3r5x
PubMed
UniProtQ81Q29|DDL_BACAN D-alanine--D-alanine ligase (Gene Name=ddl)

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