Structure of PDB 2dem Chain A Binding Site BS04

Receptor Information

>2dem Chain A (length=219) Species: 300852 (Thermus thermophilus HB8)

MDREAFVQTLTACRLCPRLVAWREEVVGRKRAFRGEPYWARPVPGFGDPE
ARILLFGLAPGAHGSNRTGRPFTGDASGAFLYPLLHEAGLSSKPESLPGD
DLRLYGVYLTAAVRCAPPKNKPTPEELRACARWTEVELGLLPEVRVYVAL
GRIALEALLAHFGLRKSAHPFRHGAHYPLPGGRHLLASYHVSRQNTQTGR
LTREMFLEVLMEAKRLAGL

Ligand information

• Ligand ID: 2HP
• InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-1
• InChIKey: NBIIXXVUZAFLBC-UHFFFAOYSA-M
• SMILES:
  OpenEye OEToolkits 1.5.0: OP(=O)(O)[O-]
  ACDLabs 10.04: [O-]P(=O)(O)O
  CACTVS 3.341: O[P](O)([O-])=O
• Formula: H2 O4 P
• Name: DIHYDROGENPHOSPHATE ION
• DrugBank: DB02831
• PDB chain: 2dem Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2dem Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): P60 G61 S65 F72 D75
• Binding residue (residue number reindexed from 1): P60 G61 S65 F72 D75
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.2.2.-

Gene Ontology

Molecular Function

• GO:0004844 uracil DNA N-glycosylase activity
• GO:0016787 hydrolase activity
• GO:0033958 DNA-deoxyinosine glycosylase activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0097506 deaminated base DNA N-glycosylase activity

Biological Process

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

External links

• PDB: RCSB:2dem, PDBe:2dem, PDBj:2dem
• PDBsum: 2dem
• PubMed: 17870091
• UniProt: Q5SJ65|UDGB_THET8 Type-5 uracil-DNA glycosylase (Gene Name=udgb)