Structure of PDB 3raf Chain B

Receptor sequence

>3rafB (length=482) Species: 1313 (Streptococcus pneumoniae)

NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDS
NTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMH
GNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEP
TVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKID
KLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKE
QIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIEL
KKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAH
RREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAK
ENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAI
IGDERTMYNLMKKELREVKKKFATPRLSSLED

3D structure

• PDB: 3raf Inhibitor-stabilised cleavage complexes of topoisomerase IIa: structural analysis of drug-dependent inter- and intramolecular interactions
• Chain: B
• Resolution: 3.24 Å

Enzymatic activity

• Enzyme Commision number: 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).

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	R28 K38 V40 H74 H76 G77 S80 R87 K93 I170	R26 K36 V38 H72 H74 G75 S78 R85 K91 I168
BS02	dna	B	Y118 I170 S171 G173 Y174 A175	Y116 I168 S169 G171 Y172 A173
BS03	MG	B	T319 Q322	T317 Q320

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
• GO:0005524 ATP binding

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006265 DNA topological change

Cellular Component

• GO:0005694 chromosome

External links

• PDB: RCSB:3raf, PDBe:3raf, PDBj:3raf
• PDBsum: 3raf
• UniProt: P72525|PARC_STRPN DNA topoisomerase 4 subunit A (Gene Name=parC)