Structure of PDB 3i12 Chain D Binding Site BS01

Receptor Information
>3i12 Chain D (length=355) Species: 90371 (Salmonella enterica subsp. enterica serovar Typhimurium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHVN
DAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDVI
FPIVHGTLGEDGSLQGMLRVANLPFVGSDVLSSAACMDKDVAKRLLRDAG
LNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANEA
QYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVLNSE
FYIDDNGAQVVVPAQIPSEVNDKIRAIAIQAYQTLGCAGMARVDVFLTAD
NEVVINEINTLPGFTNISMYPKLWQASGLGYTDLISRLIELALERHTANN
ALKTT
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 chain3i12 Chain D Residue 365 [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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PDB3i12 The crystal structure of the D-alanyl-alanine synthetase A from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Resolution2.2 Å
Binding residue
(original residue number in PDB)		K141 F183 K185 S191 S192 E221 Q222 G223 I224 E228 F304 E315
Binding residue
(residue number reindexed from 1)		K139 F181 K183 S189 S190 E219 Q220 G221 I222 E226 F296 E307
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E16 V19 Q22 H107 S191 Y260 D263 R300 D302 E315 N317 G321 I325
Catalytic site (residue number reindexed from 1) E14 V17 Q20 H105 S189 Y252 D255 R292 D294 E307 N309 G313 I317
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:3i12, PDBe:3i12, PDBj:3i12
PDBsum3i12
PubMed
UniProtP0A1F0|DDLA_SALTY D-alanine--D-alanine ligase A (Gene Name=ddlA)

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