1JCY

Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium

Structural Biology Knowledgebase: 1JCY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 1JCY

Classification: LYASE

Total Structure Weight: 60437.29

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 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
R5P
Query on R5P

A RIBOSE-5-PHOSPHATE
C5 H11 O8 P
PPQRONHOSHZGFQ-LMVFSUKVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEP
Query on PEP

A, B PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-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)
PO4
Query on PO4

B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.202
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 84.32 α = 90.00
b = 84.32 β = 90.00
c = 159.57 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