1LRU

Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin

Structural Biology Knowledgebase: 1LRU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Observed: 0.240

Literature

Macromolecules
Sequence Display for 1LRU

Classification: HYDROLASE

Total Structure Weight: 59223.98

Macromolecule Entities
Molecule Chains Length Organism Details
PEPTIDE DEFORMYLASE A, B, C 168 Escherichia coli EC#: 3.5.1.88 IUBMB
Gene Name(s): def fms b3287 JW3248
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BB2
Query on BB2

A, B, C ACTINONIN
2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1- (2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)- 2-METHYL-PROPYL]-AMIDE (Synonym)
C19 H35 N3 O5
XJLATMLVMSFZBN-VYDXJSESSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BB2 IC50: 6 - 140 nM (99 - 100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Observed: 0.240
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 141.04 α = 90.00
b = 63.61 β = 123.35
c = 83.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-05-16
  • Released Date: 2002-07-24
  • Deposition author(s): Guilloteau, J.-P., Mathieu, M., Giglione, C., Blanc, V., Dupuy, A., Chevrier, M., Gil, P., Famechon, A., Meinnel, T., Mikol, V.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4