MolNFT v1 · #77291 · protein + DNA
Quinazolinedione-DNA cleavage complex of type IV topoisomerase from S. pneumoniae
3RAF · DNA topoisomerase 4 subunit a: “Quinazolinedione-DNA cleavage complex of type IV topoisomerase from S. pneumoniae”. X-ray diffraction, 2 ligands (PDQ, MG), 12 pockets (best druggability 0.84). MolNFT v1 #77291 on GenesisL1: 3D…
- PDB
- 3RAF
- Type
- protein + DNA
- Length
- 1,418 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
- 12 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 482 | 50% helix, 18% strand | P72525 |
| C | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 208 | 46% helix, 14% strand | Q59961 |
| D | DNA topoisomerase 4 subunit B (EC 5.99.1.-) | protein | 210 | 47% helix, 15% strand | Q59961 |
| E | 5'-D(*CP*AP*TP*GP*AP*AP*T)-3' | dna | 7 | — | — |
| F | 5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3' | dna | 11 | — | — |
| G | 5'-D(*CP*GP*TP*GP*CP*AP*T)-3' | dna | 7 | — | — |
| H | 5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*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 · 4 copies · chains A, B, C, E, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.84 | 0.85 | 120 | MG, PDQ |
| 2 | 317 | 0.77 | 0.88 | 47 | MG, PDQ |
| 3 | 682 | 0.68 | 0.77 | 75 | empty |
| 4 | 645 | 0.67 | 0.76 | 64 | empty |
| 5 | 311 | 0.66 | 0.82 | 31 | empty |
Interfaces
21 interfaces between chains.
- A–B · 1505 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1505 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1496 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 721 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 714 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3RAF · Quinazolinedione-DNA cleavage complex of type IV topoisomerase from S. pneumoniae · the same entry in another collection · chain H against H, TM-score 1.00
- 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 0.97
- 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 0.96
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 3RAF · PDBe 3RAF · UniProt P72525 · UniProt Q59961
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