Structure of PDB 3d4v Chain B Binding Site BS02

Receptor Information

>3d4v Chain B (length=282) Species: 562 (Escherichia coli)

MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTA
IPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGA
ARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFP
EYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPG
DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTP
AQIRRYAERWKPWRSYALLHIWYTEGWQPDEA

Ligand information

>3d4v Chain F (length=12)

ggcactcatgtc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d4v Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): L125 K177 P213 G214 G216 W218 T219
• Binding residue (residue number reindexed from 1): L125 K177 P213 G214 G216 W218 T219

Enzymatic activity

• Catalytic site (original residue number in PDB): W218 Y222 D238
• Catalytic site (residue number reindexed from 1): W218 Y222 D238
• Enzyme Commision number: 3.2.2.21: DNA-3-methyladenine glycosylase II.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0003905 alkylbase DNA N-glycosylase activity
• GO:0005515 protein binding
• GO:0008725 DNA-3-methyladenine glycosylase activity
• GO:0016787 hydrolase activity
• GO:0032131 alkylated DNA binding
• GO:0043916 DNA-7-methylguanine glycosylase activity
• GO:0052821 DNA-7-methyladenine glycosylase activity
• GO:0052822 DNA-3-methylguanine glycosylase activity

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0006285 base-excision repair, AP site formation
• GO:0006307 DNA alkylation repair
• GO:0006950 response to stress
• GO:0006974 DNA damage response

Cellular Component

• GO:0005737 cytoplasm
• GO:0032993 protein-DNA complex

External links

• PDB: RCSB:3d4v, PDBe:3d4v, PDBj:3d4v
• PDBsum: 3d4v
• PubMed: 18686953
• UniProt: P04395|3MG2_ECOLI DNA-3-methyladenine glycosylase 2 (Gene Name=alkA)