Structure of PDB 5bpf Chain D Binding Site BS01

Receptor Information
>5bpf Chain D (length=296) Species: 632 (Yersinia pestis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQL
KEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRT
KLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHSVG
MSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRI
QPPGVFYSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQ
DRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD
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 chain5bpf Chain D 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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PDB5bpf Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		K97 I142 K144 S151 M154 E180 W182 L183 E187 F209 Y210 M259 E270
Binding residue
(residue number reindexed from 1)		K97 I142 K144 S148 M151 E177 W179 L180 E184 F206 Y207 M249 E260
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E15 V18 L21 H63 R255 D257 E270 N272 G276 H280
Catalytic site (residue number reindexed from 1) E15 V18 L21 H63 R245 D247 E260 N262 G266 H270
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:5bpf, PDBe:5bpf, PDBj:5bpf
PDBsum5bpf
PubMed26894530
UniProtQ8ZIE7|DDL_YERPE D-alanine--D-alanine ligase (Gene Name=ddl)

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