Structure of PDB 1nh3 Chain A

Receptor sequence

>1nh3A (length=471) Species: 9606 (Homo sapiens)

WKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPK
AEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDF
TQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIAN
FKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWK
EVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKK
CVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTV
GCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQ
LFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQL
KELTAPDENIPAKILSYNRANRAVSKLNYLDPRITVAWCKKWGVPIEKIY
NKTQREKFAWAIDMADEDYEF

3D structure

• PDB: 1nh3 Structural Impact of the Leukemia Drug 1-beta-D-Arabinofuranosylcytosine (Ara-C) on the Covalent Human Topoisomerase I-DNA Complex
• Chain: A
• Resolution: 3.1 Å

Enzymatic activity

• Enzyme Commision number: 5.6.2.1: DNA topoisomerase.

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	A	T411 W412 I424 Y426 M428 K436 K439 K443 K532 N722 Y723	T209 W210 I222 Y224 M226 K234 K237 K241 K330 N428 Y429
BS02	dna	A	H266 R364 N722 Y723	H64 R162 N428 Y429
BS03	dna	A	K354 E356 F361 H367 K374 K425 R488 A489 G490 N491 K493 T501 K532 T585 A586 K587 N745	K152 E154 F159 H165 K172 K223 R286 A287 G288 N289 K291 T299 K330 T383 A384 K385 N451

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003917 DNA topoisomerase type I (single strand cut, ATP-independent) activity

Biological Process

• GO:0006265 DNA topological change

Cellular Component

• GO:0005694 chromosome

External links

• PDB: RCSB:1nh3, PDBe:1nh3, PDBj:1nh3
• PDBsum: 1nh3
• PubMed: 12533542
• UniProt: P11387|TOP1_HUMAN DNA topoisomerase 1 (Gene Name=TOP1)