3TOZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with 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, E
A, B, C, D, E, F, G, H
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 
I [auth A]
L [auth B]
P [auth C]
S [auth D]
T [auth E]
I [auth A],
L [auth B],
P [auth C],
S [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth H]
J [auth A]
K [auth A]
M [auth B]
N [auth B]
BA [auth H],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
W [auth F],
Y [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth H],
Q [auth C],
R [auth C],
U [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.13α = 90
b = 78.434β = 90.49
c = 214.829γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
BALBESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    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