2024-09-28_00000025|ligand|8QMB

Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin; X-ray diffraction 2.00Å
Protein #1 742 residues (98% resolved)

MKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTLEEATVFHMSNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLEDTAKALEHHHHHH

MKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTLEEATVFHMSNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLEDTAKALEHHHHHH
DNA #2 7 bases

(DT)(DG)(DT)(DG)(DG)(DA)(DT)

TGTGGAT
DNA #3 11 bases

(DG)(DG)(DT)(DT)(DA)(DT)(DC)(DC)(DA)(DC)(DA)

GGTTATCCACA
DNA #4 7 bases

(DG)(DT)(DA)(DA)(DT)(DA)(DC)

GTAATAC
DNA #5 11 bases

(DA)(DA)(DC)(DC)(DG)(DT)(DA)(DT)(DT)(DA)(DC)

AACCGTATTAC
Non polymer #6 ACT

InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1

CC(=O)[O-]
Non polymer #7 CL

InChI=1S/ClH/h1H/p-1

[Cl-]
Non polymer #8 FMT

InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)

C(=O)O
Non polymer #9 MG

InChI=1S/Mg/q+2

[Mg+2]
Non polymer #10 MLA

InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)

C(C(=O)O)C(=O)O
Non polymer #11 MPD

InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1

C[C@@H](CC(C)(C)O)O
Non polymer #12 TE9

InChI=1S/C18H12ClF3N4O4/c19-12-13-7(1-9(20)14(12)25-3-6(27)4-25)15(28)8(18(29)30)5-26(13)17-11(22)2-10(21)16(23)24-17/h1-2,5-6,27H,3-4H2,(H2,23,24)(H,29,30)

c1c2c(c(c(c1F)N3CC(C3)O)Cl)N(C=C(C2=O)C(=O)O)c4c(cc(c(n4)N)F)F
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Reference