3TNL

1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with Shikimate and NAD.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with Shikimate and NAD.

Minasov, G.Light, S.H.Halavaty, A.Shuvalova, L.Papazisi, L.Anderson, W.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Shikimate dehydrogenase
A, B, C, D
315Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: aroElmo0490
EC: 1.1.1.25
UniProt
Find proteins for Q8Y9N5 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y9N5 
Go to UniProtKB:  Q8Y9N5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y9N5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
M [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SKM
Query on SKM

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C]
(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID
C7 H10 O5
JXOHGGNKMLTUBP-HSUXUTPPSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth C],
N [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.851α = 90
b = 82.878β = 90.03
c = 101.26γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
BALBESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description