Structure of PDB 5dg0 Chain A

Receptor sequence

>5dg0A (length=276) Species: 9606 (Homo sapiens)

ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDIL
CLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKV
SYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAF
RKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGE
LLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLL
PALCDSKIRSKALGSDHCPITLYLAL

3D structure

• PDB: 5dg0 Capturing snapshots of APE1 processing DNA damage.
• Chain: A
• Resolution: 1.8 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): N68 D70 E96 Y171 D210 N212 D283 D308 H309
• Catalytic site (residue number reindexed from 1): N26 D28 E54 Y129 D168 N170 D241 D266 H267
• Enzyme Commision number: 3.1.11.2: exodeoxyribonuclease III.
  3.1.21.-

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	Y128 Y171 N174 R177 R181 N212 N222 N226 N229 F266 M271 K276 V278 W280	Y86 Y129 N132 R135 R139 N170 N180 N184 N187 F224 M229 K234 V236 W238
BS02	dna	A	D70 G71 R73 A74 K78 K98 E126 K224 Y269 M270	D28 G29 R31 A32 K36 K56 E84 K182 Y227 M228
BS03	MN	A	D70 E96	D28 E54
BS04	MN	A	G225 N229	G183 N187

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:5dg0, PDBe:5dg0, PDBj:5dg0
• PDBsum: 5dg0
• PubMed: 26458045
• UniProt: P27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)