6TI3

Apo-SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with D-Threonine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into nucleophile substrate specificity in variants of N-Serine hydroxymethyltransferase from Streptococcus thermophilus

Petrillo, G.Hernandez, K.Bujons, J.Clapes, P.Uson, I.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferaseA,
B [auth C],
C [auth B],
D
416Streptococcus thermophilusMutation(s): 1 
Gene Names: glyACDA68_00974DID82_07515
EC: 2.1.2.1
UniProt
Find proteins for Q5M0B4 (Streptococcus thermophilus (strain CNRZ 1066))
Explore Q5M0B4 
Go to UniProtKB:  Q5M0B4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5M0B4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTH (Subject of Investigation/LOI)
Query on DTH

Download Ideal Coordinates CCD File 
F [auth A],
H [auth C],
J [auth B],
L [auth D]
D-THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-STHAYSLISA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
K [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.393α = 90
b = 113.692β = 94.51
c = 133.147γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
XPREPdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description