Structure of PDB 6w4i Chain B

Receptor sequence
>6w4iB (length=276) Species: 9606 (Homo sapiens) [Search protein sequence]
ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDIL
CLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKV
SYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAF
RKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGE
LLQAVPLADSFRHLYPNTPYAYTFWTAMMNARSKNVGWRLDYFLLSHSLL
PALCDSKIRSKALGSDHCPITLYLAL
3D structure
PDB6w4i AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.
ChainB
Resolution2.2 Å
3D
structure
Catalytic site residues are labeled in the structure
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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 B Y171 N174 R177 D210 N212 N222 N226 N229 F266 V278 W280 H309 Y129 N132 R135 D168 N170 N180 N184 N187 F224 V236 W238 H267
BS02 dna B E96 K125 Y171 E54 K83 Y129
BS03 dna B D70 G71 R73 A74 K78 K98 E126 G127 R177 M270 D28 G29 R31 A32 K36 K56 E84 G85 R135 M228
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

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Molecular Function
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Biological Process
External links
PDB RCSB:6w4i, PDBe:6w4i, PDBj:6w4i
PDBsum6w4i
PubMed32542366
UniProtP27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)

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