Research workbench
Crystal structure of streptococcus pneumonia pare with inhibitor
Analyse Crystal structure of streptococcus pneumonia pare with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YIG
- Type
- protein
- Length
- 386 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit B
- EC
- 5.99.1.3
- UniProt
- G6JAH7
- Ligands
- 54B
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 192 | 31% helix, 31% strand | G6JAH7 |
| B | DNA topoisomerase 4 subunit B (EC 5.99.1.3) | protein | 194 | 31% helix, 30% strand | G6JAH7 |
Ligands and binding sites
- 54B · 1-ethyl-3-[5-[2-[(1S,5R)-3-methyl-3,8-diazabicyclo[3.2.1]octan-8-yl]-5-(2-oxidanylidene-3H-1,3,4-oxadiazol-5-yl)pyridin-3-yl]-4-[4-(trifluoromethyl)-1,3-thiazol-2-yl]pyridin-2-yl]urea · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.69 | 0.75 | 70 | empty |
| 2 | 126 | 0.51 | 0.80 | 24 | 54B |
| 3 | 108 | 0.48 | 0.80 | 26 | 54B |
Interfaces
1 interface between chains.
- A–B · 274 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5YIG · Crystal structure of Streptococcus pneumonia ParE with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 G6JAH7
- Elsewhere: RCSB PDB 5YIG · PDBe 5YIG · UniProt G6JAH7
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