Structure of PDB 2zdg Chain B Binding Site BS01

Receptor Information
>2zdg Chain B (length=303) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKAL
TALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGK
PYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPF
FVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEV
GVLGNVFGEASPVGEVRYEAELLIPAPLDTQETVQELALKAYKVLGVRGM
ARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVEL
ALT
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 chain2zdg Chain B Residue 402 [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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PDB2zdg Crystal structure of D-Alanine:D-Alanine Ligase with ADP from Thermus thermophius HB8
Resolution2.2 Å
Binding residue
(original residue number in PDB)		K116 F151 K153 S160 I163 E189 A191 L192 E197 F272 N281 E282
Binding residue
(residue number reindexed from 1)		K116 F151 K153 S160 I163 E189 A191 L192 E197 F256 N265 E266
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E13 V16 L19 H82 S159 R268 D270 E282 N284 G288 T292
Catalytic site (residue number reindexed from 1) E13 V16 L19 H82 S159 R252 D254 E266 N268 G272 T276
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:2zdg, PDBe:2zdg, PDBj:2zdg
PDBsum2zdg
PubMed
UniProtQ5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)

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