Structure of PDB 6n17 Chain A

Receptor sequence
>6n17A (length=438) Species: 9606 (Homo sapiens) [Search protein sequence]
NPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWL
VKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGT
HHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHK
SGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGR
FQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKW
LCSEFKESMLTLGKESSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQT
AEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSAN
LSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGPMAT
FPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVP
3D structure
PDB6n17 Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening.
ChainA
Resolution1.639 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.1.4.-
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 K8Y A Y204 H263 K265 N283 S399 S400 P461 H493 K495 N516 Y43 H102 K104 N122 S238 S239 P295 H327 K329 N350 MOAD: ic50=1.01mM
PDBbind-CN: -logKd/Ki=3.00,IC50=1.01mM
Gene Ontology
Molecular Function
GO:0008081 phosphoric diester hydrolase activity
Biological Process
GO:0006281 DNA repair
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6n17, PDBe:6n17, PDBj:6n17
PDBsum6n17
PubMed31199869
UniProtQ9NUW8|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 (Gene Name=TDP1)

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