3AEN

Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing Michaelis complex and alpha-amino-alpha, beta-butenoic acid-pyridoxal-5'-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Entamoeba histolytica methionine gamma-lyase 1

Karaki, T.Sato, D.Shimizu, A.Nozaki, T.Harada, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine gamma-lyaseA, C389Entamoeba histolyticaMutation(s): 0 
Gene Names: metg
EC: 4.4.1.11
Find proteins for Q86D28 (Entamoeba histolytica)
Explore Q86D28 
Go to UniProtKB:  Q86D28
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine gamma-lyaseB, D389Entamoeba histolyticaMutation(s): 0 
Gene Names: metg
EC: 4.4.1.11
Find proteins for Q86D28 (Entamoeba histolytica)
Explore Q86D28 
Go to UniProtKB:  Q86D28
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4LM
Query on 4LM

Download Ideal Coordinates CCD File 
H [auth B], M [auth D](2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid
C12 H15 N2 O7 P
BBYSOXSBJOWRNU-VMTXVVAMSA-N
 Ligand Interaction
MET
Query on MET

Download Ideal Coordinates CCD File 
E [auth A]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], I [auth B], J [auth C], K [auth C], N [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A], L [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, CL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.156α = 90
b = 85.428β = 101.9
c = 114.746γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description