6B88

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)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.407 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Signal peptidase I
A, B
247Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: lepB
EC: 3.4.21.89
Find proteins for P00803 (Escherichia coli (strain K12))
Go to UniProtKB:  P00803
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CZD
Query on CZD

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Download CCD File 
A, B
(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
C47 H61 N11 O7
SJYWASAPFZIDQL-UAKBWTGGSA-N
 Ligand Interaction
1PE
Query on 1PE

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Download CCD File 
B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.407 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.238 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 109.980α = 90.00
b = 109.980β = 90.00
c = 116.250γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references, Structure summary