6H2Q

Crystal Structure of Arg184Gln mutant of Human Prolidase with Mn ions and LeuPro ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for prolidase deficiency disease mechanisms.

Wilk, P.Uehlein, M.Piwowarczyk, R.Dobbek, H.Mueller, U.Weiss, M.S.

(2018) FEBS J. 285: 3422-3441


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xaa-Pro dipeptidase
A, B
493Homo sapiensMutation(s): 1 
Gene Names: PEPD (PRD)
EC: 3.4.13.9
Find proteins for P12955 (Homo sapiens)
Go to Gene View: PEPD
Go to UniProtKB:  P12955
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
LEU
Query on LEU

Download SDF File 
Download CCD File 
A, B
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PRO
Query on PRO

Download SDF File 
Download CCD File 
A, B
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 103.559α = 90.00
b = 106.661β = 90.00
c = 217.432γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-09-26
    Type: Data collection, Database references