Structure of PDB 4l1k Chain A Binding Site BS01

Receptor Information
>4l1k Chain A (length=340) 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]
RKIRVGLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQGQWHV
NDPDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQQALAQIDVVF
PIVHGTLGEDGSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARL
AVAPFVCFDRHTAAHADVDTLIAQLGLPLFVKPANQGSSVGVSQVRTADA
FAAALALALAYDHKVLVEAAVAGREIECAVLGNAVPHASVCGEVVVEIVI
PADIDAQTQQRIQQIAVQAYQALGCAGMARVDVFLCADGRIVINEVNTLP
GFTRISVYPKLWQASGLDYRGLITRLIELALERHTDDQLL
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 chain4l1k Chain A Residue 401 [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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PDB4l1k Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K141 F183 K185 S191 S192 E221 A222 A223 V224 E228 F304 N314 E315
Binding residue
(residue number reindexed from 1)		K138 F180 K182 S188 S189 E218 A219 A220 V221 E225 F284 N294 E295
Annotation score3
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) Q21 H104 S188 R280 D282 E295 N297 G301 I305
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:4l1k, PDBe:4l1k, PDBj:4l1k
PDBsum4l1k
PubMed24440607
UniProtQ5H614

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