3DOY

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3i

Structural Biology Knowledgebase: 3DOY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.200

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DOY

Classification: LYASE

Total Structure Weight: 111068.44

Macromolecule Entities
Molecule Chains Length Organism Details
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase A, B, C..., D, E, FA, B, C, D, E, F 159 Helicobacter pylori EC#: 4.2.1.59 IUBMB
Gene Name(s): fabZ

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

A, C 4-chloro-N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]benzohydrazide
C14 H9 Br2 Cl N2 O3
ZDMUFSJTENTNDA-NGYBGAFCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BEN
Query on BEN

A, B, C, E BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D, E, F CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
2BE IC50: 1520 nM (97) BindingDB

IC50: 1520 nM  BindingMOAD
IC50: 1520 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.200
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 73.97 α = 90.00
b = 100.37 β = 90.00
c = 186.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-07
  • Released Date: 2009-05-05
  • Deposition author(s): Zhang, L., He, L., Liu, X., Liu, H., Shen, X., Jiang, H.

Revision History

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