Structure of PDB 3r5f Chain A Binding Site BS01

Receptor Information
>3r5f Chain A (length=343) Species: 291331 (Xanthomonas oryzae pv. oryzae KACC 10331) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIRVGLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQGQWHVN
DPDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQALAQIDVVFPI
VHGTLGEDGSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARLAV
APFVCFDRHTAAHADVDTLIAQLGLPLFVKPANQGSSVGVSQVRTADAFA
AALALALAYDHKVLVEAAVAGREIECAVLGNAVPHASVCGEVVVEIVIPA
DIDAQTQQRIQQIAVQAYQALGCAGMARVDVFLCADGRIVINEVNTLPGF
TRISVYPKLWQASGLDYRGLITRLIELALERHTDDQLLRSAVE
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 chain3r5f Chain A Residue 368 [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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PDB3r5f Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ATP
Resolution2.07 Å
Binding residue
(original residue number in PDB)		F183 K185 S192 A223 V224 E228 F304 E315
Binding residue
(residue number reindexed from 1)		F178 K180 S187 A218 V219 E223 F282 E293
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) Q22 H107 S191 R300 D302 E315 N317 G321 I325
Catalytic site (residue number reindexed from 1) Q20 H102 S186 R278 D280 E293 N295 G299 I303
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:3r5f, PDBe:3r5f, PDBj:3r5f
PDBsum3r5f
PubMed
UniProtQ5H614

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