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Dna gyrase atp binding domain of enterococcus faecalis in complex with a small molecule inhibitor ((3S)-1-[2-(PYRIDO[2,3-B]PYRAZIN-7-YLSULFANYL)-9H-PYRIMIDO[4,5-B]INDOL-4-YL]PYRROLIDIN-3-AMINE)

Analyse Dna gyrase atp binding domain of enterococcus faecalis in complex with a small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KTN
Type: protein
Length: 193 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.69
Source: Enterococcus faecalis
Molecule: DNA gyrase subunit B
EC: 5.99.1.3
UniProt: Q839Z1
Ligands: MJU
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · resolution 1.69 · 1 distinct chain · 30% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA gyrase subunit B (EC 5.99.1.3)	protein	193	30% helix, 30% strand	Q839Z1

Ligands and binding sites

MJU · (3S)-1-[2-(pyrido[2,3-b]pyrazin-7-ylsulfanyl)-9H-pyrimido[4,5-b]indol-4-yl]pyrrolidin-3-amine · 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	113	0.49	0.80	23	MJU

Compared structures

4KTN · DNA gyrase ATP binding domain of enterococcus faecalis in complex with a small molecule… · the same entry in another collection · chain A against A, TM-score 1.00
Q839Z1 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (Q839Z1) · 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 Q839Z1
Elsewhere: RCSB PDB 4KTN · PDBe 4KTN · UniProt Q839Z1

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