Structure of PDB 6w3q Chain B

Receptor sequence
>6w3qB (length=276) Species: 9606 (Homo sapiens) [Search protein sequence]
ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDIL
CLQETKCSENKRPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKV
SYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAF
RKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGE
LLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLL
PALCDSKIRSKALGSDHCPITLYLAL
3D structure
PDB6w3q Molecular and structural characterization of disease-associated APE1 polymorphisms.
ChainB
Resolution2.49 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 N222 N226 M271 K276 N180 N184 M229 K234
BS02 dna B E96 Y128 Y171 N174 N212 A230 F266 E54 Y86 Y129 N132 N170 A188 F224
BS03 dna B D70 G71 R73 A74 K78 K103 E126 Y269 M270 D28 G29 R31 A32 K36 K61 E84 Y227 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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6w3q, PDBe:6w3q, PDBj:6w3q
PDBsum6w3q
PubMed32454397
UniProtP27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)

[Back to BioLiP]