8DU1

Crystal Structure of NAD bound dTDP-glucose 4,6-dehydratase from Elizabethkingia anophelis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis

DeBouver, N.D.Abendroth, J.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
dTDP-glucose 4,6-dehydratase
A, B, C, D
367Elizabethkingia anophelis NUHP1Mutation(s): 0 
Gene Names: BD94_3274
EC: 4.2.1.46
UniProt
Find proteins for A0A077ELH2 (Elizabethkingia anophelis NUHP1)
Explore A0A077ELH2 
Go to UniProtKB:  A0A077ELH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A077ELH2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
Q [auth C],
W [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
G [auth A]
H [auth A]
J [auth B]
L [auth B]
E [auth A],
G [auth A],
H [auth A],
J [auth B],
L [auth B],
M [auth B],
P [auth C],
R [auth C],
S [auth C],
V [auth D],
X [auth D],
Y [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
T [auth C],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
O [auth C],
U [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.74α = 90
b = 84.62β = 101.18
c = 130.87γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Data collection