MolNFT v1 · #141504 · protein

S.AUREUS gyrb ATPase domain in complex with 4,6-dichloro-2- (METHYLTHIO)PYRIMIDINE

5Z9N · DNA gyrase subunit B: “S.AUREUS gyrb ATPase domain in complex with 4,6-dichloro-2- (METHYLTHIO)PYRIMIDINE”. X-ray diffraction, 2 ligands (HX5, SO4), 1 pocket (best druggability 0.52). MolNFT v1 #141504 on GenesisL1: 3D structure…

PDB: 5Z9N
Type: protein
Length: 189 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA gyrase subunit B
EC: 5.99.1.3
UniProt: P0AES6
Ligands: HX5, SO4
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA gyrase subunit B (EC 5.99.1.3)	protein	189	29% helix, 31% strand	P0AES6

Ligands and binding sites

HX5 · 4,6-dichloro-2-(methylsulfanyl)pyrimidine · ligand · chains A
SO4 · Sulfate ion · ion · 4 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	111	0.52	0.82	23	HX5

Compared structures

5Z9N · S.aureus GyrB ATPase domain in complex with 4,6-dichloro-2-(methylthio)pyrimidine · the same entry in another collection · chain A against A, TM-score 1.00
P0AES6 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0AES6) · 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 P0AES6
Elsewhere: RCSB PDB 5Z9N · PDBe 5Z9N · UniProt P0AES6

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