Structure of PDB 5wn2 Chain A Binding Site BS04

Receptor Information
>5wn2 Chain A (length=276) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDIL
CLQQTKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKV
SYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAF
RKFLKGLASRKPLVLCGNLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGE
LLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLL
PALCDSKIRSKALGSDHCPITLYLAL
Ligand information
Ligand IDPGA
InChIInChI=1S/C2H5O6P/c3-2(4)1-8-9(5,6)7/h1H2,(H,3,4)(H2,5,6,7)
InChIKeyASCFNMCAHFUBCO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C(C(=O)O)OP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OCC(=O)O
FormulaC2 H5 O6 P
Name2-PHOSPHOGLYCOLIC ACID
ChEMBLCHEMBL47181
DrugBankDB02726
ZINCZINC000003869735
PDB chain5wn2 Chain D Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5wn2 Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Resolution2.288 Å
Binding residue
(original residue number in PDB)		Q96 Y171 N174 N212 F266
Binding residue
(residue number reindexed from 1)		Q54 Y129 N132 N170 F224
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) N68 Q96 N210 N212 D283 D308 H309
Catalytic site (residue number reindexed from 1) N26 Q54 N168 N170 D241 D266 H267
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5wn2, PDBe:5wn2, PDBj:5wn2
PDBsum5wn2
PubMed29374164
UniProtP27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)

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