1EEX

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

Structural Biology Knowledgebase: 1EEX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.161

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1EEX

Classification: LYASE

Total Structure Weight: 210882.68

Macromolecule Entities
Molecule Chains Length Organism Details
PROPANEDIOL DEHYDRATASE A, L 554 Klebsiella oxytoca EC#: 4.2.1.28 IUBMB
Fragment: ALPHA CHAIN
Gene Name(s): pddA pduC AB185_12495 SK88_04876 SK91_02751
PROPANEDIOL DEHYDRATASE B, E 224 Klebsiella oxytoca EC#: 4.2.1.28 IUBMB
Fragment: BETA CHAIN
Gene Name(s): pddB
PROPANEDIOL DEHYDRATASE G, M 173 Klebsiella oxytoca EC#: 4.2.1.28 IUBMB
Fragment: GAMMA CHAIN
Gene Name(s): pddC pduE AB185_12485 KOJKO3_c4550 SK91_02753

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

A, L CO-(ADENIN-9-YL-PENTYL)-COBALAMIN
C72 H106 Co N18 O14 P
KWGNLVVAVJCVFN-AFACOYQJDT
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGO
Query on PGO

A, L S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, L POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.161
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 73.38 α = 90.00
b = 121.40 β = 90.00
c = 207.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-02-04
  • Released Date: 2001-02-07
  • Deposition author(s): Shibata, N., Masuda, J., Toraya, T., Morimoto, Y., Yasuoka, N.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4