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Gyrase B in complex with 4,5-dibromopyrrolamide-based inhibitor

Analyse Gyrase B in complex with 4,5-dibromopyrrolamide-based inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZVI
Type: protein
Length: 357 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: P0AES7
Ligands: 4S4, IOD
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA gyrase subunit B (EC 5.99.1.3)	protein	357	40% helix, 26% strand	P0AES7

Ligands and binding sites

4S4 · N-(4-{[(4,5-dibromo-1H-pyrrol-2-yl)carbonyl]amino}benzoyl)glycine · ligand · chains A
IOD · Iodide ion · ion · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	418	0.58	0.74	50	empty
2	107	0.52	0.82	18	4S4

Compared structures

4ZVI · Gyrase B in complex with 4,5-dibromopyrrolamide-based inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P0AES7 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0AES7) · 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 P0AES7
Elsewhere: RCSB PDB 4ZVI · PDBe 4ZVI · UniProt P0AES7

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