5F2M

Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with competitive inhibitor hexitol-1,6-bisphosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

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

NON-STEREOSPECIFIC SUBSTRATE CLEAVAGE BY TAGATOSE-BISPHOSPHATE CLASS I ALDOLASE

LowKam, C., Liotard, B., Sygusch, J.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tagatose 1,6-diphosphate aldolase 2
A, B, C, D
327Streptococcus pyogenes serotype M1Mutation(s): 0 
Gene Names: lacD2, lacD.2, SPy_1919, M5005_Spy1635
EC: 4.1.2.40
UniProt
Find proteins for P63705 (Streptococcus pyogenes serotype M1)
Explore P63705 
Go to UniProtKB:  P63705
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63705
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M2P
Query on M2P
Download Ideal Coordinates CCD File 
E [auth A]D-MANNITOL-1,6-DIPHOSPHATE
C6 H16 O12 P2
WOYYTQHMNDWRCW-KVTDHHQDSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth B]
J [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth D],
O [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.985α = 90
b = 107.837β = 90
c = 237.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2016-12-07 
    • Deposition Author(s): LowKam, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description