1PHW

Crystal structure of KDO8P synthase in its binary complex with substrate analog 1-deoxy-A5P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.313
  • R-Value Work: 0.237

Literature

Macromolecules
Sequence Display for 1PHW

Classification: TRANSFERASE

Total Structure Weight: 31084.79

Macromolecule Entities
Molecule Chains Length Organism Details
2-dehydro-3-deoxyphosphooctonate aldolase A 284 Escherichia coli EC#: 2.5.1.55 IUBMB
Gene Name(s): kdsA b1215 JW1206
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
N
Query on N

A ANY 5'-MONOPHOSPHATE NUCLEOTIDE
1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE (Synonym)
C5 H11 O7 P
CYZZKTRFOOKUMT-LMVFSUKVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
N N/A in BindingDB
Ki: 500000 nM  BindingMOAD
Ki: 500000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.313
  • R-Value Work: 0.237
  • Space Group: I 2 3

Unit Cell:

Length (Å) Angle (°)
a = 118.26 α = 90.00
b = 118.26 β = 90.00
c = 118.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-29
  • Released Date: 2004-07-13
  • Deposition author(s): Vainer, R., Belakhov, V., Rabkin, E., Baasov, T., Adir, N.

Revision History

  • Version 1_0: 2004-07-13

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance