MolNFT v1 · #181019 · protein + DNA
K. pneumoniae topoisomerase IV (pare-parc) in complex with DNA and (3S)-10-[(3R)-3-(1-AMINOCYCLOPROPYL)PYRROLIDIN-1-yl]-9-fluoro-3- methyl-5-oxo-2,3-dihydro-5H-[1,4]OXAZINO[2,3,4-IJ]QUINOLINE-6- carboxylic acid (compound 25)
7LHZ · DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit…: “K. pneumoniae topoisomerase IV (pare-parc) in complex with DNA and…”. X-ray diffraction, 2 ligands (Y21, MG), 20 pockets (best druggability 0.87). MolNFT v1 #181019 on…
- PDB
- 7LHZ
- Type
- protein + DNA
- Length
- 2,820 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 chimera; DNA…
- EC
- 5.6.2.2
- UniProt
- A0A377Y395, A0A486EJ79
- Ligands
- Y21, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit a chimera (EC 5.6.2.2) | protein | 714 | 46% helix, 15% strand | A0A377Y395, A0A486EJ79 |
| D | DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit a chimera (EC 5.6.2.2) | protein | 677 | 47% helix, 13% strand | A0A377Y395, A0A486EJ79 |
| A | DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit a chimera (EC 5.6.2.2) | protein | 706 | 46% helix, 15% strand | A0A377Y395, A0A486EJ79 |
| B | DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit a chimera (EC 5.6.2.2) | protein | 631 | 50% helix, 12% strand | A0A377Y395, A0A486EJ79 |
| P, J | DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3') | dna | 10 | — | — |
| K | DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)- 3') | dna | 15 | — | — |
| I | DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)- 3') | dna | 14 | — | — |
| G, F | DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)- 3') | dna | 13 | — | — |
| H | DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3') | dna | 8 | — | — |
| E | DNA (5'-D(P*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3') | dna | 9 | — | — |
Ligands and binding sites
- Y21 · (3S)-10-[(3R)-3-(1-aminocyclopropyl)pyrrolidin-1-yl]-9-fluoro-3-methyl-5-oxo-2,3-dihydro-5H-[1,4]oxazino[2,3, 4-ij]quinoline-6-carboxylic acid · ligand · 4 copies · chains D, K, I, J, C, P, A, B, G, F, E, H
- MG · Magnesium ion · metal · 4 copies · chains C, D, A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains C, A
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 | 1004 | 0.87 | 0.89 | 123 | MG, Y21 |
| 2 | 1172 | 0.87 | 0.88 | 137 | MG, Y21 |
| 3 | 667 | 0.84 | 0.89 | 68 | empty |
| 4 | 431 | 0.81 | 0.89 | 56 | empty |
| 5 | 538 | 0.81 | 0.87 | 62 | empty |
Interfaces
22 interfaces between chains.
- A–B · 1869 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1843 Ų buried · 20 hydrogen bonds · protein-protein
- A–G · 821 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–I · 796 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–K · 795 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 7LHZ · K. pneumoniae Topoisomerase IV (ParE-ParC) in complex with DNA and… · 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 A0A377Y395
- Every structure of UniProt A0A486EJ79
- Elsewhere: RCSB PDB 7LHZ · PDBe 7LHZ · UniProt A0A377Y395 · UniProt A0A486EJ79
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