Structure of PDB 6w2p Chain A

Receptor sequence

>6w2pA (length=276) Species: 9606 (Homo sapiens)

ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDIL
CLQETKCSENKRPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKV
SYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAF
RKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGE
LLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLL
PALCDSKIRSKALGSDHCPITLYLAL

3D structure

• PDB: 6w2p Molecular and structural characterization of disease-associated APE1 polymorphisms.
• Chain: A
• Resolution: 1.94 Å

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 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	Y171 N174 R177 D210 N212 N222 N226 N229 A230 F266 M271 K276 V278 W280 L282 H309	Y129 N132 R135 D168 N170 N180 N184 N187 A188 F224 M229 K234 V236 W238 L240 H267
BS02	dna	A	Y128 R177	Y86 R135
BS03	dna	A	D70 G71 R73 A74 K78 E126 Y269 M270 M271	D28 G29 R31 A32 K36 E84 Y227 M228 M229

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:6w2p, PDBe:6w2p, PDBj:6w2p
• PDBsum: 6w2p
• PubMed: 32454397
• UniProt: P27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)