5MC3

Crystal Structure of Glu412Lys mutant of Human Prolidase with Mn ions and GlyPro ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
484Homo 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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

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Download CCD File 
A, B
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

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A, B
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
PRO
Query on PRO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.131 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 103.590α = 90.00
b = 106.412β = 90.00
c = 217.434γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XDSdata scaling
XSCALEdata scaling
PHENIXrefinement
XSCALEdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-08-15
    Type: Data collection, Database references
  • Version 1.2: 2018-09-26
    Type: Data collection, Database references