4PTN

Crystal Structure of YagE, a KDG aldolase protein in complex with Magnesium cation coordinated L-glyceraldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.

Manicka, S.Peleg, Y.Unger, T.Albeck, S.Dym, O.Greenblatt, H.M.Bourenkov, G.Lamzin, V.Krishnaswamy, S.Sussman, J.L.

(2008) Proteins 71: 2102-2108


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable 2-keto-3-deoxy-galactonate aldolase YagE
A, B, C, D
343Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yagE
EC: 4.1.2.51
Find proteins for P75682 (Escherichia coli (strain K12))
Go to UniProtKB:  P75682
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

Download SDF File 
Download CCD File 
B, D
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
A, B, C, D
L-glyceraldehyde
(2S)-2,3-dihydroxypropanal
C3 H6 O3
MNQZXJOMYWMBOU-GSVOUGTGSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 141.200α = 90.00
b = 155.070β = 90.00
c = 55.400γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release