1JYM

Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design

Structural Biology Knowledgebase: 1JYM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.296
  • R-Value Work: 0.231

Literature

Macromolecules
Sequence Display for 1JYM

Classification: HYDROLASE

Total Structure Weight: 218809.56

Macromolecule Entities
Molecule Chains Length Organism Details
Peptide Deformylase A, B, C..., D, E, F, G, H, I, JA, B, C, D, E, F, G, H, I, J 183 Plasmodium falciparum EC#: 3.5.1.88 IUBMB
Gene Name(s): PFI0380c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CO
Query on CO

A, B, C, D, E, F, G, H, I, J COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.296
  • R-Value Work: 0.231
  • Space Group: P 41
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 121.26 α = 90.00
b = 121.26 β = 90.00
c = 177.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-12
  • Released Date: 2002-03-13
  • Deposition author(s): Kumar, A., Nguyen, K.T., Srivathsan, S., Ornstein, B., Turley, S., Hirsh, I., Pei, D., Hol, W.G.J.

Revision History

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