4E9B

Structure of Peptide Deformylase form Helicobacter Pylori in complex with actinonin

Structural Biology Knowledgebase: 4E9B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 4E9B

Classification: HYDROLASE / HYDROLASE INHIBTIOR

Total Structure Weight: 21847.64

Macromolecule Entities
Molecule Chains Length Organism Details
Peptide deformylase 11 A 181 Helicobacter pylori EC#: 3.5.1.88 IUBMB
Fragment: UNP RESIDUES 2-164
Gene Name(s): def
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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)
EPE
Query on EPE

A 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CO
Query on CO

A COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.188
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 41.39 α = 90.00
b = 51.78 β = 90.00
c = 91.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-20
  • Released Date: 2013-04-24
  • Deposition author(s): Cui, K., Zhu, L., Lu, W., Huang, J.

Revision History

No revisions since initial release