3CEP

Structure of a tryptophan synthase quinonoid intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate.

Barends, T.R.Domratcheva, T.Kulik, V.Blumenstein, L.Niks, D.Dunn, M.F.Schlichting, I.

(2008) Chembiochem 9: 1024-1028


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase alpha chainA268Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: trpA
EC: 4.2.1.20
UniProt
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P00929 
Go to UniProtKB:  P00929
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase beta chainB396Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: trpB
EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A2K1 
Go to UniProtKB:  P0A2K1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
H [auth B]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
G3P (Subject of Investigation/LOI)
Query on G3P

Download Ideal Coordinates CCD File 
C [auth A]SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N
 Ligand Interaction
CS
Query on CS

Download Ideal Coordinates CCD File 
E [auth B], F [auth B], G [auth B]CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
IDM
Query on IDM

Download Ideal Coordinates CCD File 
D [auth A], J [auth B]INDOLINE
C8 H9 N
LPAGFVYQRIESJQ-UHFFFAOYSA-N
 Ligand Interaction
MH6
Query on MH6

Download Ideal Coordinates CCD File 
I [auth B]3-hydroxy-2-iminopropanoic acid
C3 H5 N O3
MUHXUPVPXJXCGV-DUXPYHPUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.024α = 90
b = 58.908β = 95.19
c = 67.086γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2014-12-17
    Changes: Experimental preparation