2GN8

Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADP and UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.209

Literature

Macromolecules
Sequence Display for 2GN8

Classification: LYASE

Total Structure Weight: 79939.79

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-GlcNAc C6 dehydratase A, B 344 Helicobacter pylori EC#: 4.2.1.115 IUBMB
Gene Name(s): pseB flaA1 HP_0840
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 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)
UDP
Query on UDP

A, B URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

A 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-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: 0.245
  • R-Value Work: 0.209
  • Space Group: P 63

Unit Cell:

Length (Å) Angle (°)
a = 111.06 α = 90.00
b = 111.06 β = 90.00
c = 107.79 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-04-09
  • Released Date: 2006-05-09
  • Deposition author(s): Ishiyama, N., Creuzenet, C., Lam, J.S., Berghuis, A.M.

Revision History

  • Version 1_0: 2006-05-09

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance

  • Version 1_3: 2017-10-18

    Type: Refinement description