Structure of PDB 6u1k Chain D Binding Site BS05

Receptor Information
>6u1k Chain D (length=320) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKAL
TALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGK
PYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKEPPVVPFDPPFF
VKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVG
VLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQ
ELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEA
GGVAYPELLRRLVELALTHH
Ligand information
Ligand IDCO3
InChIInChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-2
InChIKeyBVKZGUZCCUSVTD-UHFFFAOYSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(=O)([O-])[O-]
ACDLabs 10.04
CACTVS 3.341		[O-]C([O-])=O
FormulaC O3
NameCARBONATE ION
ChEMBL
DrugBankDB14531
ZINC
PDB chain6u1k Chain D Residue 407 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6u1k d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		S159 K228 E282 N284
Binding residue
(residue number reindexed from 1)		S158 K227 E281 N283
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) V16 L19 H82 E226 R268 G288 T292
Catalytic site (residue number reindexed from 1) V16 L19 H82 E225 R267 G287 T291
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:6u1k, PDBe:6u1k, PDBj:6u1k
PDBsum6u1k
PubMed32335509
UniProtQ5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)

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