MolNFT v1 · #70750 · protein + DNA
Inhibitor-stabilized topoisomerase IV-DNA cleavage complex (S. pneumoniae)
3LTN · DNA topoisomerase 4 subunit a: “Inhibitor-stabilized topoisomerase IV-DNA cleavage complex (S. pneumoniae)”. X-ray diffraction, 2 ligands (PDQ, MG), 17 pockets (best druggability 0.84). MolNFT v1 #70750 on GenesisL1: 3D structure…
- PDB
- 3LTN
- Type
- protein + DNA
- Length
- 1,442 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit a; DNA topoisomerase 4 subunit B…
- EC
- 5.99.1.-
- UniProt
- P72525, Q59961
- Ligands
- PDQ, MG
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 481 | 48% helix, 17% strand | P72525 |
| C, D | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 222 | 41% helix, 18% strand | Q59961 |
| E | 5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*T)-3' | dna | 7 | — | — |
| F | 5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*G P*T)-3' | dna | 11 | — | — |
| G | 5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*T)-3' | dna | 7 | — | — |
| H | 5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*A P*G)-3' | dna | 11 | — | — |
Ligands and binding sites
- PDQ · 3-amino-7-{(3R)-3-[(1S)-1-aminoethyl]pyrrolidin-1-yl}-1-cyclopropyl-6-fluoro-8-methylquinazoline-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B, C, E, F, H, D, G
- MG · Magnesium ion · metal · 2 copies · chains C, E, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.84 | 0.85 | 101 | PDQ |
| 2 | 498 | 0.78 | 0.86 | 60 | empty |
| 3 | 128 | 0.76 | 0.95 | 22 | MG |
| 4 | 769 | 0.75 | 0.80 | 82 | MG |
| 5 | 1070 | 0.73 | 0.77 | 106 | empty |
Interfaces
22 interfaces between chains.
- B–D · 1587 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1582 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1558 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 896 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 894 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3LTN · Inhibitor-stabilized topoisomerase IV-DNA cleavage complex (S. pneumoniae) · the same entry in another collection · chain H against H, TM-score 1.00
- P72525 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit a (P72525) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q59961 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit B (Q59961) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P72525
- Every structure of UniProt Q59961
- Elsewhere: RCSB PDB 3LTN · PDBe 3LTN · UniProt P72525 · UniProt Q59961
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