Structure of PDB 6u1d Chain A Binding Site BS01

Receptor Information
>6u1d Chain A (length=324) 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
FEAGGVAYPELLRRLVELALTHHH
Ligand information
Ligand IDDAL
InChIInChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1
InChIKeyQNAYBMKLOCPYGJ-UWTATZPHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C(=O)O)N
CACTVS 3.341C[CH](N)C(O)=O
CACTVS 3.341C[C@@H](N)C(O)=O
ACDLabs 10.04O=C(O)C(N)C
OpenEye OEToolkits 1.5.0C[C@H](C(=O)O)N
FormulaC3 H7 N O2
NameD-ALANINE
ChEMBLCHEMBL66693
DrugBankDB01786
ZINCZINC000004658556
PDB chain6u1d Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6u1d d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		E13 H82 Y229 R268
Binding residue
(residue number reindexed from 1)		E15 H84 Y231 R270
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:6u1d, PDBe:6u1d, PDBj:6u1d
PDBsum6u1d
PubMed32335509
UniProtQ5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)

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