1Q1Y

Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin

Structural Biology Knowledgebase: 1Q1Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 1Q1Y

Classification: Hydrolase

Total Structure Weight: 22143.76

Macromolecule Entities
Molecule Chains Length Organism Details
Peptide deformylase A 191 Staphylococcus aureus EC#: 3.5.1.88 IUBMB
Mutation: C111X, N171D
Gene Name(s): def def1 pdf1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 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)
ZN
Query on ZN

A 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: 20 nM (99) BindingDB

N/A in BindingMoad
IC50: 20 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSD
Query on CSD
A L-PEPTIDE LINKING C3 H7 N O4 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.205
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.42 α = 90.00
b = 120.84 β = 90.00
c = 48.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-07-23
  • Released Date: 2004-07-23
  • Deposition author(s): Yoon, H.J., Lee, S.K., Kim, H.L., Kim, H.W., Kim, H.W., Lee, J.Y., Mikami, B., Suh, S.W.

Revision History

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