3ZCZ

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a trifluoroketone inhibitor

Structural Biology Knowledgebase: 3ZCZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 3ZCZ

Classification: HYDROLASE

Total Structure Weight: 193845.59

Macromolecule Entities
Molecule Chains Length Organism Details
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE A, B, C, D 467 Actinomadura sp. r39 EC#: 3.4.16.4 IUBMB
Fragment: RESIDUES 50-516
Gene Name(s): dac
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D (2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro- 3-hydroxybutan-2-yl]amino}heptanoic acid
C11 H19 F3 N2 O4
GCYIIHHJPYOBBJ-BHNWBGBOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TFR N/A in BindingDB
N/A in BindingMoad
Ki: 170 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.193
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 103.65 α = 90.00
b = 91.73 β = 94.30
c = 106.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-23
  • Released Date: 2013-03-27
  • Deposition author(s): Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

Revision History

  • 2013-08-28
    Type: Citation | Details: JRNL