Structure of PDB 3q1k Chain B Binding Site BS01

Receptor Information
>3q1k Chain B (length=346) 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]
AKLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKTRFDVVLLGIDKAGQWHV
NDAENYLQNADDPAHIALRPSAISLAQVPGKHQHQLINAQNGQPLPTVDV
IFPIVHGTLGEDGSLQGMLRVANLPFVGSDVLSSAACMDKDVAKRLLRDA
GLNIAPFITLTRTNRHAFSFAEVESRLGLPLFVKPANQGSSVGVSKVANE
AQYQQAVALAFEFDHKVVVEQGIKGREIECAVLGNDNPQASTCGEIVLAQ
VVVPAQIPSEVNDKIRAIAIQAYQTLGCAGMARVDVFLTADNEVVINEIN
TLPGFTNISMYPKLWQASGLGYTDLISRLIELALERHTANNALKTT
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 chain3q1k Chain B Residue 370 [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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PDB3q1k The Crystal Structure of the D-alanyl-alanine Synthetase A from Salmonella enterica Typhimurium Complexed with ADP
Resolution2.202 Å
Binding residue
(original residue number in PDB)		K141 F183 K185 S191 S192 G223 I224 E228 F304 E315
Binding residue
(residue number reindexed from 1)		K140 F182 K184 S190 S191 G222 I223 E227 F287 E298
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E16 V19 Q22 H107 S191 R300 D302 E315 N317 G321 I325
Catalytic site (residue number reindexed from 1) E15 V18 Q21 H106 S190 R283 D285 E298 N300 G304 I308
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:3q1k, PDBe:3q1k, PDBj:3q1k
PDBsum3q1k
PubMed
UniProtP0A1F0|DDLA_SALTY D-alanine--D-alanine ligase A (Gene Name=ddlA)

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