Structure of PDB 5wn5 Chain A Binding Site BS01

Receptor Information

>5wn5 Chain A (length=273) Species: 9606 (Homo sapiens)

ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDIL
CLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKV
SYGIGDHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRK
FLKGLARKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQ
AVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPAL
CDSKIRSKALGSDHCPITLYLAL

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 5wn5 Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wn5 Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): D70 E96
• Binding residue (residue number reindexed from 1): D28 E54
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): N68 E96 D210 N212 D283 D308 H309
• Catalytic site (residue number reindexed from 1): N26 E54 D165 N167 D238 D263 H264
• Enzyme Commision number: 3.1.11.2: exodeoxyribonuclease III.
  3.1.21.-

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0004518 nuclease activity
• GO:0004519 endonuclease activity

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:5wn5, PDBe:5wn5, PDBj:5wn5
• PDBsum: 5wn5
• PubMed: 29374164
• UniProt: P27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)