2YPO

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with phenylalanine bound in only one site

Structural Biology Knowledgebase: 2YPO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.159
  • R-Value Work: 0.138

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YPO

Classification: TRANSFERASE

Total Structure Weight: 102874.78

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG A, B 462 Mycobacterium tuberculosis EC#: 2.5.1.54 IUBMB
Gene Name(s): aroG Rv2178c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PHE
Query on PHE

A, B PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PHE N/A in BindingDB
Kd: 21000 nM  BindingMOAD
Kd: 21000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.159
  • R-Value Work: 0.138
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 203.97 α = 90.00
b = 203.97 β = 90.00
c = 66.60 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-31
  • Released Date: 2013-01-09
  • Deposition author(s): Blackmore, N.J., Reichau, S., Jiao, W., Hutton, R.D., Baker, E.N., Jameson, G.B., Parker, E.J.

Revision History

  • 2013-05-08
    Type: Citation | Details: JRNL
  • 2013-05-08
    Type: Refinement description | Details: REMARK 3