1PE1

Aquifex aeolicus KDO8PS in complex with cadmium and 2-PGA

Structural Biology Knowledgebase: 1PE1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1PE1

Classification: LYASE

Total Structure Weight: 60336.17

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

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

A, B 2-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
GXIURPTVHJPJLF-UWTATZPHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

A, B CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.193
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 84.43 α = 90.00
b = 84.43 β = 90.00
c = 159.75 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-20
  • Released Date: 2004-02-03
  • Deposition author(s): Wang, J., Xu, X., Grison, C., Petek, S., Coutrot, P., Birck, M.R., Woodard, R.W., Gatti, D.L.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4