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MolNFT v1 · #168253 · protein + DNA

K. pneumoniae topoisomerase IV (pare-parc) in complex with DNA and compound 34 (7-[(1S,5R)-1-amino-3-AZABICYCLO[3.1.0]HEXAN-3-yl]-4- (aminomethyl)-1-cyclopropyl-3,6-difluoro-8-methylquinolin-2(1H)-one)

6WAA · DNA topoisomerase 4 subunit B,DNA topoisomerase (ATP…: “K. pneumoniae topoisomerase IV (pare-parc) in complex with DNA and compound 34…”. X-ray diffraction, 3 ligands (TNJ, MG, CL), 20 pockets (best druggability 0.87). MolNFT v1…

PDB
6WAA
Type
protein + DNA
Length
2,798 residues
Chains
12
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA topoisomerase 4 subunit B,DNA topoisomerase (ATP- hydrolyzing) chimera; DNA…
EC
5.6.2.2
UniProt
A0A377Y395, A0A377XIN8
Ligands
TNJ, MG, CL
Pockets
20 · best druggability 0.87

Structure

x-ray diffraction · 10 distinct chains · 48% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA topoisomerase 4 subunit B,DNA topoisomerase (ATP- hydrolyzing) chimera (EC 5.6.2.2)protein70248% helix, 16% strandA0A377Y395, A0A377XIN8
DDNA topoisomerase 4 subunit B,DNA topoisomerase (ATP- hydrolyzing) chimera (EC 5.6.2.2)protein63750% helix, 12% strandA0A377Y395, A0A377XIN8
FDNA topoisomerase 4 subunit B,DNA topoisomerase (ATP- hydrolyzing) chimera (EC 5.6.2.2)protein70747% helix, 16% strandA0A377Y395, A0A377XIN8
HDNA topoisomerase 4 subunit B,DNA topoisomerase (ATP- hydrolyzing) chimera (EC 5.6.2.2)protein65649% helix, 13% strandA0A377Y395, A0A377XIN8
I, PDNA (5'-D(*TP*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')dna9——
JDNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)- 3')dna14——
K, NDNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)- 3')dna15——
LDNA (5'-D(*TP*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')dna10——
MDNA (5'-D(*TP*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')dna11——
ODNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)- 3')dna13——

Ligands and binding sites

  • TNJ · 7-[(1S,5R)-1-amino-3-azabicyclo[3.1.0]hexan-3-yl]-4-(aminomethyl)-1-cyclopropyl-3,6-difluoro-8-methylquinolin-2(1H)-one · ligand · 4 copies · chains B, D, I, J, K, L, F, H, N, O, P, M
  • MG · Magnesium ion · metal · 11 copies · chains B, J, I, D, L, F, N, M, H, K, O, P
  • CL · Chloride ion · ion · 2 copies · chains B, H
  • MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains B, J, D, K, F, H, O

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
17980.870.90106MG, TNJ
29580.850.8688MG, MPD, TNJ
34660.810.8953empty
47210.810.8567MG
55170.810.8848empty

Interfaces

26 interfaces between chains.

  • F–H · 2404 Ų buried · 27 hydrogen bonds · protein-protein
  • B–D · 2124 Ų buried · 23 hydrogen bonds · protein-protein
  • B–J · 934 Ų buried · 14 hydrogen bonds · protein-nucleic
  • F–N · 932 Ų buried · 14 hydrogen bonds · protein-nucleic
  • D–K · 930 Ų buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

  • 6WAA · K. pneumoniae Topoisomerase IV (ParE-ParC) in complex with DNA and compound 34… · the same entry in another collection · chain I against I, TM-score 1.00

Analyse

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