1MMF

Crystal structure of substrate free form of glycerol dehydratase

Structural Biology Knowledgebase: 1MMF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.228

Literature

Macromolecules
Sequence Display for 1MMF

Classification: Lyase

Total Structure Weight: 199133.41

Macromolecule Entities
Molecule Chains Length Organism Details
glycerol dehydrase 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 dehydrase beta subunit B, E 194 Klebsiella pneumoniae EC#: 4.2.1.30 IUBMB
Mutation: M1V
Gene Name(s): gldB AFK73_02945
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
glycerol dehydrase 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 2 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)
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: 2.5 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.228
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.70 α = 90.00
b = 110.07 β = 107.64
c = 114.69 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-09-03
  • Released Date: 2003-06-10
  • Deposition author(s): Liao, D.I., Dotson, G., Turner, I., Reiss, L., Emptage, M.

Revision History

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