6RNG

Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

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

Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase

Wojciechowska, I.Vogeli, B.Shahar, A.Szlachetko, J.Gorka, M.Sokolowska, E.M.Veyel, D.Silva, D.V.Erb, T.Zarivach, R.Skirycz, A.

Not Published 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fructose-bisphosphate aldolase 6, cytosolicA,
B,
C [auth F],
D [auth G]
358Arabidopsis thalianaMutation(s): 0 
Gene Names: FBA6At2g36460
EC: 4.1.2.13
UniProt
Find proteins for Q9SJQ9 (Arabidopsis thaliana)
Explore Q9SJQ9 
Go to UniProtKB:  Q9SJQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SJQ9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRO
Query on PRO

Download Ideal Coordinates CCD File 
M [auth B],
U [auth G],
W [auth G]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth B]
G [auth B]
H [auth B]
I [auth B]
E [auth A],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
N [auth F],
O [auth F],
P [auth G],
Q [auth G],
R [auth G],
S [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GLY
Query on GLY

Download Ideal Coordinates CCD File 
L [auth B],
T [auth G],
V [auth G]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.399α = 90
b = 73.164β = 106.52
c = 176.225γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description