1LM6

Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae

Structural Biology Knowledgebase: 1LM6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 1LM6

Classification: HYDROLASE

Total Structure Weight: 24378.79

Macromolecule Entities
Molecule Chains Length Organism Details
peptide deformylase DEFB A 215 Streptococcus pneumoniae EC#: 3.5.1.88 IUBMB
Mutation: C130X
Gene Name(s): def SP_1456
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
OCS
Query on OCS
A L-PEPTIDE LINKING C3 H7 N O5 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.208
  • Space Group: P 43

Unit Cell:

Length (Å) Angle (°)
a = 49.71 α = 90.00
b = 49.71 β = 90.00
c = 91.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-04-30
  • Released Date: 2003-06-24
  • Deposition author(s): Kreusch, A., Spraggon, G., Lee, C.C., Klock, H., McMullan, D., Ng, K., Shin, T., Vincent, J., Warner, I., Ericson, C., Lesley, S.A.

Revision History

  • 2014-11-12
    Type: Polymer description | Details: Change CSW to OCS
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update