MolNFT v1 · #122975 · protein + DNA
AMP-pnp-stabilized ATPase domain of topoisomerase IV from streptococcus pneumoniae, complex type II
5J5Q · DNA topoisomerase 4 subunit B: “AMP-pnp-stabilized ATPase domain of topoisomerase IV from streptococcus pneumoniae, complex type II”. X-ray diffraction, 2 ligands (ANP, MG), 17 pockets (best druggability 0.83). MolNFT v1 #122975 on…
- PDB
- 5J5Q
- Type
- protein + DNA
- Length
- 1,609 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit B; DNA (5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3')
- EC
- 5.99.1.3
- UniProt
- Q59961
- Ligands
- ANP, MG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 396 | 36% helix, 26% strand | Q59961 |
| C | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 394 | 35% helix, 25% strand | Q59961 |
| D | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 395 | 36% helix, 26% strand | Q59961 |
| E, F | DNA (5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3') | dna | 14 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 5 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.83 | 0.91 | 72 | ANP, MG |
| 2 | 461 | 0.82 | 0.89 | 61 | ANP, MG |
| 3 | 339 | 0.82 | 0.91 | 59 | ANP, MG |
| 4 | 858 | 0.80 | 0.84 | 66 | ANP |
| 5 | 514 | 0.78 | 0.85 | 78 | ANP, MG |
Interfaces
7 interfaces between chains.
- A–B · 2939 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2662 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 685 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- B–E · 254 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–F · 246 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5J5Q · AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae… · the same entry in another collection · chain F against F, 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 B against A, TM-score 0.98
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 Q59961
- Elsewhere: RCSB PDB 5J5Q · PDBe 5J5Q · UniProt Q59961
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