5E33

Structure of human DPP3 in complex with met-enkephalin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.182

Literature

Macromolecules
Sequence Display for 5E33

Classification: HYDROLASE

Total Structure Weight: 82275.47

Macromolecule Entities
Molecule Chains Length Organism Details
Dipeptidyl peptidase 3 A 726 Homo sapiens EC#: 3.4.14.4 IUBMB
Mutation: C19S, E207C, E451A, S491C, C519S, C654S
Gene Name(s): DPP3 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Met-enkephalin B 5 Homo sapiens Gene Name(s): PENK Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.182
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 119.79 α = 90.00
b = 105.76 β = 93.49
c = 65.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-10-01
  • Released Date: 2016-04-13
  • Deposition author(s): Kumar, P., Reithofer, V., Reisinger, M., Pavkov-Keller, T., Wallner, S., Macheroux, P., Gruber, K.

Revision History

  • Version 1_0: 2016-04-13

    Type: Initial release

  • Version 2_0: 2017-09-06

    Type: Atomic model, Author supporting evidence