Structure of PDB 6u1k Chain B Binding Site BS03

Receptor Information

>6u1k Chain B (length=322) Species: 300852 (Thermus thermophilus HB8)

MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKAL
TALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGK
PYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPF
FVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEV
GVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETV
QELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFE
AGGVAYPELLRRLVELALTHHH

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 6u1k Chain B Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6u1k d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): E282 N284
• Binding residue (residue number reindexed from 1): E282 N284
• Annotation score: 1

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 E226 R268 G288 T292
• 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

External links

• PDB: RCSB:6u1k, PDBe:6u1k, PDBj:6u1k
• PDBsum: 6u1k
• PubMed: 32335509
• UniProt: Q5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)