Structure of PDB 2b9s Chain A

Receptor sequence

>2b9sA (length=426) Species: 5661 (Leishmania donovani)

DLNWWEQENLRIAMKGERRWETLAHNGVLFPPEYEPHGIPIFYDGREFKM
TPEEEEVATMFAVMKEHDYYRMEVFRRNFFESWREILDKRQHPIRRLELC
DFEPIYQWHLVQREKKLSRTKEEKKAIKEKQDAEAEPYRYCVWDGRREQV
ANFRVEPPGLFRGRGKHPLMGKLKVRVQPEDITINIGETAEVPVPPAGHK
WAAVQHDHTVTWLAMWRDSVAGNMKYVMLAPSSSVKGQSDMVKFEKARKL
KDKVDDIRASYMEDFKSNDLHVAQRAVAMYFIDRLALRVGNEKGEDEADT
VGCCSLRVEHIQLMPDNIVRFDFLGKDSIRYQNDVAVLPEVYALLQRFTR
RKSPGMDIFDQLNPTQLNDHLKSFMDGLSAKVFRTYNASITLDRWFKEKP
WSTADKLAYFNKANTEVAILCNHQKS

3D structure

• PDB: 2b9s The Structure of the Transition State of the Heterodimeric Topoisomerase I of Leishmania donovani as a Vanadate Complex with Nicked DNA.
• Chain: A
• Resolution: 2.27 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	K41 V236 T237 W238 M250 Y252 K269 K352 K407	K15 V210 T211 W212 M224 Y226 K243 K326 K381
BS02	dna	A	H93 R190 R314 K352 D353 I355 H453 Q454 S456	H67 R164 R288 K326 D327 I329 H423 Q424 S426
BS03	dna	A	E182 F187 R188 R190 H193 K200 K251 V315 G316 N317 K319 T326 K352 D353 N394 K398 S405 A406 K407	E156 F161 R162 R164 H167 K174 K225 V289 G290 N291 K293 T300 K326 D327 N368 K372 S379 A380 K381
BS04	VO4	A	R314 R410 H453	R288 R384 H423

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:2b9s, PDBe:2b9s, PDBj:2b9s
• PDBsum: 2b9s
• PubMed: 16487540
• UniProt: Q9GPZ9