5D02

Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Glu176Gln variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Glu176Gln variant at 1.87 Angstroms resolution

Heyes, L.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospho-2-dehydro-3-deoxyheptonate aldolase
A, B, C, D
351Neisseria meningitidis MC58Mutation(s): 1 
Gene Names: aroGNMB0307
EC: 2.5.1.54
UniProt
Find proteins for Q9K169 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9K169 
Go to UniProtKB:  Q9K169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K169
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEP
Query on PEP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
Q [auth D]
PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
S [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth B],
K [auth B],
N [auth C],
O [auth C],
R [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
P [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.54α = 90
b = 135.546β = 96.27
c = 76.009γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-08-10 
  • Deposition Author(s): Heyes, L.C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations