1FY6

AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH CADMIUM AND A5P

Structural Biology Knowledgebase: 1FY6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 1FY6

Classification: LYASE

Total Structure Weight: 60291.15

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 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
A5P
Query on A5P

A ARABINOSE-5-PHOSPHATE
C5 H13 O8 P
VJDOAZKNBQCAGE-WDCZJNDASA-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

A, 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: 1.89 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.219
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 84.67 α = 90.00
b = 84.67 β = 90.00
c = 160.04 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-09-28
  • Released Date: 2001-04-21
  • Deposition author(s): Duewel, H.S., Radaev, S., Wang, J., 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