4DR9

Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin

Structural Biology Knowledgebase: 4DR9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.182

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DR9

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 87537.98

Macromolecule Entities
Molecule Chains Length Organism Details
Peptide deformylase A, B, C, D 192 Synechococcus elongatus EC#: 3.5.1.88 IUBMB
Gene Name(s): def syc0213_d

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

A, B, C, D 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BR
Query on BR

A, B, C, D BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BB2 N/A in BindingDB
IC50: 10 nM  BindingMOAD
IC50: 10 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.182
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 43.25 α = 80.87
b = 65.78 β = 76.82
c = 68.29 γ = 82.75

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-17
  • Released Date: 2013-01-16
  • Deposition author(s): Lorimer, D., Abendroth, J., Craig, T., Burgin, A., Segall, A., Rohwler, F.

Revision History

  • 2013-07-10
    Type: Citation | Details: Citation update
  • 2013-06-05
    Type: Citation | Details: Citation update
  • 2013-03-06
    Type: Citation | Details: Citation update