1B4E

X-ray structure of 5-aminolevulinic acid dehydratase complexed with the inhibitor levulinic acid

Structural Biology Knowledgebase: 1B4E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 1B4E

Classification: LYASE

Total Structure Weight: 36414.54

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE) A 323 Escherichia coli EC#: 4.2.1.24 IUBMB
Mutation: I5S, C134K
Gene Name(s): hemB ncf b0369 JW0361
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SHF
Query on SHF

A LAEVULINIC ACID
LEVULINIC ACID (Synonym)
C5 H8 O3
JOOXCMJARBKPKM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.188
  • Space Group: I 4 2 2

Unit Cell:

Length (Å) Angle (°)
a = 126.70 α = 90.00
b = 126.70 β = 90.00
c = 141.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-12-19
  • Released Date: 1999-12-17
  • Deposition author(s): Erskine, P.T., Cooper, J.B., Lewis, G., Spencer, P., Wood, S.P., Shoolingin-Jordan, P.M.

Revision History

  • 2012-01-18
    Type: Non-polymer description | Details: --
  • 2012-01-18
    Type: Linkage | Details: --
  • 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