MolNFT v1 · #114402 · protein

Crystal structure of streptococcus pneumonia pare inhibitor

5BOD · DNA topoisomerase 4 subunit B: “Crystal structure of streptococcus pneumonia pare inhibitor”. X-ray diffraction, 1 ligand (TTJ), 1 pocket (best druggability 0.46). MolNFT v1 #114402 on GenesisL1: 3D structure, binding sites and…

PDB: 5BOD
Type: protein
Length: 192 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA topoisomerase 4 subunit B
EC: 5.99.1.3
UniProt: Q8DQB5
Ligands: TTJ
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA topoisomerase 4 subunit B (EC 5.99.1.3)	protein	192	32% helix, 30% strand	Q8DQB5

Ligands and binding sites

TTJ · (2R)-N-[3-(3,5-dimethylphenyl)-1H-pyrazol-5-yl]-1,4-dioxane-2-carboxamide · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	88	0.46	0.81	16	TTJ

Compared structures

5BOD · Crystal structure of Streptococcus pneumonia ParE 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 Q8DQB5
Elsewhere: RCSB PDB 5BOD · PDBe 5BOD · UniProt Q8DQB5

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