Structure of PDB 3rad Chain A

Receptor sequence

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

NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDS
NTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMH
GNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEP
TVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKID
KLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKE
QIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIEL
KKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAH
RREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAK
ENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAI
IGDERTMYNLMKKELREVKKKFATPRLSSLED

3D structure

• PDB: 3rad Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones.
• Chain: A
• Resolution: 3.35 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	A	R28 K38 H74 H76 R87 I170	R26 K36 H72 H74 R85 I168
BS02	dna	A	Y118 I170 S171 A172 G173 Y174 A175 N326	Y116 I168 S169 A170 G171 Y172 A173 N324
BS03	MG	A	K317 T319 Q322	K315 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:3rad, PDBe:3rad, PDBj:3rad
• PDBsum: 3rad
• PubMed: 27655731
• UniProt: P72525|PARC_STRPN DNA topoisomerase 4 subunit A (Gene Name=parC)