4XED

PKD domain of M14-like peptidase from Thermoplasmatales archaeon SCGC AB-540-F20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.169
  • R-Value Work: 0.138

Literature

Macromolecules
Sequence Display for 4XED

Classification: PROTEIN BINDING

Total Structure Weight: 11263.07

Macromolecule Entities
Molecule Chains Length Organism Details
Peptidase M14, carboxypeptidase A A 99 Thermoplasmatales archaeon scgc ab-540-f20 Fragment: PKD domain residues 667-762
Gene Name(s): MBGDF03_00742
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 46.19 α = 90.00
b = 48.87 β = 90.00
c = 78.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-12-23
  • Released Date: 2015-05-13
  • Deposition author(s): Michalska, K., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2015-05-13

    Type: Initial release

  • Version 1_1: 2017-09-20

    Type: Advisory, Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy, Structure summary