MolNFT v1 · #122974 · protein + DNA
AMP-pnp-stabilized ATPase domain of topoisomerase IV from streptococcus pneumoniae, complex type I
5J5P · DNA topoisomerase 4 subunit B: “AMP-pnp-stabilized ATPase domain of topoisomerase IV from streptococcus pneumoniae, complex type I”. X-ray diffraction, 3 ligands (ANP, MG, NA), 9 pockets (best druggability 0.81). MolNFT v1 #122974…
- PDB
- 5J5P
- Type
- protein + DNA
- Length
- 817 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*GP*CP*GP*C)-3')
- EC
- 5.99.1.3
- UniProt
- Q59961
- Ligands
- ANP, MG, NA
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 397 | 37% helix, 25% strand | Q59961 |
| B | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 396 | 37% helix, 25% strand | Q59961 |
| C, D, E, F | DNA (5'-D(*GP*CP*GP*CP*GP*C)-3') | dna | 6 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.81 | 0.97 | 35 | ANP, MG |
| 2 | 154 | 0.81 | 0.97 | 35 | ANP, MG |
| 3 | 737 | 0.81 | 0.85 | 63 | MG |
| 4 | 511 | 0.76 | 0.84 | 44 | MG |
| 5 | 124 | 0.43 | 0.76 | 23 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2980 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 353 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–E · 323 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–F · 289 Ų buried · 26 hydrogen bonds · nucleic-nucleic
- C–D · 283 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 5J5P · 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 0.97
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 5J5P · PDBe 5J5P · UniProt Q59961
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