Structure of PDB 6u1f Chain A Binding Site BS05

Receptor Information
>6u1f Chain A (length=325) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEMRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEK
ALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELL
GKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDP
PFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVREL
EVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQE
TVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRL
FEAGGVAYPELLRRLVELALTHHHH
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 chain6u1f Chain A Residue 407 [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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PDB6u1f d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K116 F151 K153 G158 S159 S160 I163 L192 E197 Y223 K228 F272 N281 E282
Binding residue
(residue number reindexed from 1)		K118 F153 K155 G160 S161 S162 I165 L194 E199 Y225 K230 F274 N283 E284
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) V16 L19 H82 E226 R268 G288 T292
Catalytic site (residue number reindexed from 1) V18 L21 H84 E228 R270 G290 T294
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:6u1f, PDBe:6u1f, PDBj:6u1f
PDBsum6u1f
PubMed32335509
UniProtQ5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)

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