Structure of PDB 1rfi Chain B

Receptor sequence
>1rfiB (length=429) Species: 9606 (Homo sapiens) [Search protein sequence]
NPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWL
VKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGT
HHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHK
SGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGR
FQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKW
LCSEFKESMLTLGSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQ
NWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKA
AWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKFFTFPVPYDLPP
ELYGSKDRPWIWNIPYVKAPDTHGNMWVP
3D structure
PDB1rfi Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes.
ChainB
Resolution2.2 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 dna B Y204 F259 H263 G402 S403 P461 K469 S518 A520 Y43 F98 H102 G241 S242 P291 K299 S348 A350
BS02 peptide B Y204 C205 H237 I285 G458 S459 P461 H493 Y43 C44 H76 I124 G288 S289 P291 H323
BS03 VO4 B H263 K265 H493 K495 H102 K104 H323 K325 BindingDB: IC50=4000nM
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:1rfi, PDBe:1rfi, PDBj:1rfi
PDBsum1rfi
PubMed14761185
UniProtQ9NUW8|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 (Gene Name=TDP1)

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