Structure of PDB 5bph Chain B Binding Site BS01

Receptor Information
>5bph Chain B (length=305) Species: 632 (Yersinia pestis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLK
EQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTK
LVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEGSS
VGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSI
RIQPPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCS
GWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARI
LMLAD
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain5bph Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5bph Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		K97 I142 K144 E180 W182 L183 E187 V208 Y210 M259 E270
Binding residue
(residue number reindexed from 1)		K96 I141 K143 E179 W181 L182 E186 V207 Y209 M258 E269
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E15 V18 L21 H63 S150 D213 Y216 R255 D257 E270 N272 G276 H280
Catalytic site (residue number reindexed from 1) E14 V17 L20 H62 S149 D212 Y215 R254 D256 E269 N271 G275 H279
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:5bph, PDBe:5bph, PDBj:5bph
PDBsum5bph
PubMed26894530
UniProtQ8ZIE7|DDL_YERPE D-alanine--D-alanine ligase (Gene Name=ddl)

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