MolNFT v1 · #117795 · protein + DNA
Quinolone-stabilized cleavage complex of topoisomerase IV from klebsiella pneumoniae
5EIX · DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit a: “Quinolone-stabilized cleavage complex of topoisomerase IV from klebsiella pneumoniae”. X-ray diffraction, 2 ligands (LFX, MG), 20 pockets (best druggability 0.84). MolNFT…
- PDB
- 5EIX
- Type
- protein + DNA
- Length
- 2,833 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit a; Symmetrised E-site (pre-cut)
- EC
- 5.99.1.3
- UniProt
- R4YHS8, R4YE07
- Ligands
- LFX, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit a (EC 5.99.1.3) | protein | 702 | 45% helix, 15% strand | R4YHS8, R4YE07 |
| E, C, H, K | Symmetrised E-site (pre-cut) | dna | 8 | — | — |
| F, D, I, L | Symmetrised E-site (pre-cut) | dna | 12 | — | — |
| B | DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit a (EC 5.99.1.3) | protein | 701 | 45% helix, 15% strand | R4YHS8, R4YE07 |
| G | DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit a (EC 5.99.1.3) | protein | 671 | 45% helix, 15% strand | R4YHS8, R4YE07 |
| J | DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit a (EC 5.99.1.3) | protein | 679 | 46% helix, 13% strand | R4YHS8, R4YE07 |
Ligands and binding sites
- LFX · (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid · ligand · 4 copies · chains A, E, F, G, I, B, C, D, J, L, H, K
- MG · Magnesium ion · metal · 8 copies · chains A, G, F, I, B, J, D, L
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.84 | 0.87 | 89 | MG, LFX |
| 2 | 893 | 0.83 | 0.85 | 95 | MG, LFX |
| 3 | 765 | 0.81 | 0.85 | 108 | empty |
| 4 | 690 | 0.80 | 0.85 | 62 | empty |
| 5 | 424 | 0.78 | 0.87 | 62 | empty |
Interfaces
24 interfaces between chains.
- A–G · 2291 Ų buried · 30 hydrogen bonds · protein-protein
- B–J · 2077 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 814 Ų buried · 10 hydrogen bonds · protein-nucleic
- J–L · 811 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–F · 801 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 5EIX · Quinolone-stabilized cleavage complex of topoisomerase IV from klebsiella pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt R4YHS8
- Every structure of UniProt R4YE07
- Elsewhere: RCSB PDB 5EIX · PDBe 5EIX · UniProt R4YHS8 · UniProt R4YE07
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