Structure of PDB 2dem Chain A

Receptor sequence

>2demA (length=219) Species: 300852 (Thermus thermophilus HB8)

MDREAFVQTLTACRLCPRLVAWREEVVGRKRAFRGEPYWARPVPGFGDPE
ARILLFGLAPGAHGSNRTGRPFTGDASGAFLYPLLHEAGLSSKPESLPGD
DLRLYGVYLTAAVRCAPPKNKPTPEELRACARWTEVELGLLPEVRVYVAL
GRIALEALLAHFGLRKSAHPFRHGAHYPLPGGRHLLASYHVSRQNTQTGR
LTREMFLEVLMEAKRLAGL

3D structure

• PDB: 2dem Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.
• Chain: A
• Resolution: 1.95 Å

Enzymatic activity

• Enzyme Commision number: 3.2.2.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	A59 S77 N120 G151 R152 Y189 H190 S192 R193 Q194 N195 R200	A59 S77 N120 G151 R152 Y189 H190 S192 R193 Q194 N195 R200
BS02	dna	A	K30 R31 A32 R193 Q194 Q197 T198	K30 R31 A32 R193 Q194 Q197 T198
BS03	SF4	A	C13 L15 C16 P42 C115 C130 W133	C13 L15 C16 P42 C115 C130 W133
BS04	2HP	A	P60 G61 S65 F72 D75	P60 G61 S65 F72 D75

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)