Structure of PDB 4c5c Chain B Binding Site BS01

Receptor Information
>4c5c Chain B (length=306) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQL
KSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRS
KLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGS
SVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPS
IRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGC
KGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVR
ILELAD
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 chain4c5c Chain B Residue 310 [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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PDB4c5c Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		K97 I142 K144 G149 S150 S151 M154 E180 W182 L183 E187 Y210 K215 D257 M259 L269 E270 N272
Binding residue
(residue number reindexed from 1)		K97 I142 K144 G149 S150 S151 M154 E180 W182 L183 E187 Y210 K215 D257 M259 L269 E270 N272
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E15 V18 N21 H63 S150 E213 Y216 R255 D257 E270 N272 G276 H280
Catalytic site (residue number reindexed from 1) E15 V18 N21 H63 S150 E213 Y216 R255 D257 E270 N272 G276 H280
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:0042803 protein homodimerization 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:4c5c, PDBe:4c5c, PDBj:4c5c
PDBsum4c5c
PubMed29208891
UniProtP07862|DDLB_ECOLI D-alanine--D-alanine ligase B (Gene Name=ddlB)

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