1JCX

Aquifex aeolicus KDO8P synthase in complex with API and Cadmium

Structural Biology Knowledgebase: 1JCX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 1JCX

Classification: LYASE

Total Structure Weight: 60604.56

Macromolecule Entities
Molecule Chains Length Organism Details
2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE A, B 267 Aquifex aeolicus EC#: 2.5.1.55 IUBMB
Gene Name(s): kdsA aq_085
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B {[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY- 6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID
C9 H23 N O13 P2
ATILYNKCRYHYEP-SQEXRHODSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

A, B CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PAI N/A in BindingDB
Ki: 7000 nM  BindingMOAD
Ki: 7000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.206
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 84.53 α = 90.00
b = 84.53 β = 90.00
c = 160.20 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-06-11
  • Released Date: 2002-01-16
  • Deposition author(s): Wang, J., Duewel, H.S., Woodard, R.W., Gatti, D.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values