1IWP

Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae

Structural Biology Knowledgebase: 1IWP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.209

Literature

Macromolecules
Sequence Display for 1IWP

Classification: LYASE

Total Structure Weight: 199349.72

Macromolecule Entities
Molecule Chains Length Organism Details
Glycerol Dehydratase Alpha subunit A, L 555 Klebsiella pneumoniae EC#: 4.2.1.30 IUBMB
Gene Name(s): dhaB1 dhaB gldA pduC AC565_24705 AGG09_17405 AN412_06890 AN966_21135 AQD68_17000 AQD73_16960 CH1034_300178 KPLM21_80188 MS6671_43850 PMK1_01006 SM74_03652 SM87_03232
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Glycerol Dehydratase Beta subunit B, E 194 Klebsiella pneumoniae EC#: 4.2.1.30 IUBMB
Gene Name(s): gldB AFK73_02945
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Glycerol Dehydratase Gamma subunit G, M 141 Klebsiella pneumoniae EC#: 4.2.1.30 IUBMB
Gene Name(s): dhaB3 dhaE gldC pduE AC565_24695 AFK73_02940 AGG09_17415 AN412_06880 AN966_21145 AQD68_17010 AQD73_16970 CH1034_300176 KPLM21_80190 KpST82_0486 SM74_03650 SM87_03230
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B12
Query on B12

B, E COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGO
Query on PGO

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.209
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 81.38 α = 90.00
b = 108.22 β = 96.75
c = 113.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-05-28
  • Released Date: 2002-10-02
  • Deposition author(s): Yamanishi, M., Yunoki, M., Tobimatsu, T., Toraya, T.

Revision History

  • 2012-10-24
    Type: Non-polymer description | Details: update B12
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4