E. COLI lepb in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2- (2-(4-(tert-BUTYL)PHENYL)-4-methylpyrimidine-5-carboxamido)-N- methylbutanamido)-16,26-BIS(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl- 6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide)

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).

Ligands and binding sites

• CZD · (8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19), 2(20),3,5,15,17-hexaene-8-carboxamide · ligand · 2 copies · chains A, B
• 1PE · Pentaethylene glycol · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 394 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

• 6B88 · E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phen… · the same entry in another collection · chain B against B, TM-score 1.00
• P00803 · AlphaFold monomer V2.0 prediction for signal peptidase I (P00803) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 P00803
• Elsewhere: RCSB PDB 6B88 · PDBe 6B88 · UniProt P00803