Research workbench
Crystal structure of E. COLI topoisomerase IV pare 43KDA subunit complexed with adpnp
Analyse Crystal structure of E. COLI topoisomerase IV pare 43KDA subunit complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S16
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Topoisomerase IV subunit B
- EC
- 5.99.1.-
- UniProt
- P20083
- Ligands
- ANP, MG, SO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Topoisomerase IV subunit B (EC 5.99.1.-) | protein | 380 | 35% helix, 27% strand | P20083 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.82 | 0.97 | 35 | MG, ANP |
| 2 | 155 | 0.81 | 0.98 | 37 | MG, ANP |
| 3 | 345 | 0.71 | 0.84 | 67 | empty |
| 4 | 173 | 0.54 | 0.79 | 20 | empty |
| 5 | 135 | 0.51 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2391 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1S16 · Crystal Structure of E. coli Topoisomerase IV ParE 43kDa subunit complexed with ADPNP · the same entry in another collection · chain A against A, TM-score 1.00
- P20083 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit B (P20083) · a predicted model of the same protein · chain A 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 P20083
- Elsewhere: RCSB PDB 1S16 · PDBe 1S16 · UniProt P20083
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