Structure of PDB 3u6d Chain A Binding Site BS01

Receptor Information

>3u6d Chain A (length=252) Species: 1422 (Geobacillus stearothermophilus)

PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQT
VRGLERRGKFLKFLLDRDALISHLRMEGRYAVASALEPLEPHTHVVFCFT
DGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAER
AVKTKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIE
RLHEEMVATIGEAVMHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRC
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Ligand information

>3u6d Chain B (length=13)

ggtagatcccgac

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3u6d Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM.
• Resolution: 1.87 Å
• Binding residue (original residue number in PDB): W30 N32 V111 R112 K113 F114 T155
• Binding residue (residue number reindexed from 1): W29 N31 V110 R111 K112 F113 T154

Enzymatic activity

• Catalytic site (original residue number in PDB): P2 Q3
• Catalytic site (residue number reindexed from 1): P1 Q2
• Enzyme Commision number: 3.2.2.23: DNA-formamidopyrimidine glycosylase.
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0008270 zinc ion binding
• GO:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity
• GO:0016787 hydrolase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
• GO:0016829 lyase activity
• GO:0019104 DNA N-glycosylase activity
• GO:0034039 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
• GO:0046872 metal ion binding
• GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:3u6d, PDBe:3u6d, PDBj:3u6d
• PDBsum: 3u6d
• PubMed: 22465958
• UniProt: P84131