5WOL

Crystal structure of dihydrodipicolinate reductase DapB from Coxiella burnetii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 5WOL

Classification: OXIDOREDUCTASE

Total Structure Weight: 28082.89

Macromolecule Entities
Molecule Chains Length Organism Details
4-hydroxy-tetrahydrodipicolinate reductase A 239 Coxiella burnetii EC#: 1.17.1.8 IUBMB
Gene Name(s): dapB CBU_1709
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE (Synonym)
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PE3
Query on PE3

A 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE- 1,41-DIOL
POLYETHYLENE GLYCOL (Synonym)
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
6PC
Query on 6PC

A PYRIDINE-2-CARBOXYLIC ACID
PICOLINIC ACID (Synonym)
C6 H5 N O2
SIOXPEMLGUPBBT-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.178
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 73.61 α = 90.00
b = 78.79 β = 90.00
c = 84.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-08-02
  • Released Date: 2017-08-16
  • Deposition author(s): Stogios, P.J., Wawrzak, Z., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • Version 1_0: 2017-08-16

    Type: Initial release

  • Version 1_1: 2017-09-20

    Type: Author supporting evidence