6TGH

SHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as external aldimine and as non-covalent complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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
415Streptococcus 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EVM (Subject of Investigation/LOI)
Query on EVM

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene]
C11 H14 N2 O8 P
JFLJYKRWFQAEDK-QLKAYGNNSA-N
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
I [auth C],
M [auth D]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
DSN (Subject of Investigation/LOI)
Query on DSN

Download Ideal Coordinates CCD File 
H [auth C],
L [auth D]
D-SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-UWTATZPHSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.795α = 90
b = 112.93β = 93.1
c = 131.918γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description