Download MendeleyStructural 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.
6TI1
SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with PLP/L-Threonine/Lys230 gem diamine complex
- PDB DOI: https://doi.org/10.2210/pdb6TI1/pdb
- Classification: TRANSFERASE
- Organism(s): Streptococcus thermophilus
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2019-11-21 Released: 2020-04-29
- Funding Organization(s): Spanish Ministry of Economy and Competitiveness
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Work: 0.178
- R-Value Observed: 0.178
Starting Model: experimental
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This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Serine hydroxymethyltransferase | A, B [auth C] | 416 | Streptococcus thermophilus | Mutation(s): 1 Gene Names: glyA, CDA68_00974, DID82_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 Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5M0B4 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2BO (Subject of Investigation/LOI) Query on 2BO | D [auth A], F [auth C] | N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine C12 H19 N2 O8 P IZWQBQLGLAKRMN-XCBNKYQSSA-N |  | ||
| GOL (Subject of Investigation/LOI) Query on GOL | C [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NA (Subject of Investigation/LOI) Query on NA | E [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Work: 0.178
- R-Value Observed: 0.178
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.708 | α = 90 |
| b = 114.708 | β = 90 |
| c = 192.063 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| XPREP | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-04-29 Deposition Author(s): Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Spanish Ministry of Economy and Competitiveness | Spain | -- |
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, Derived calculations, Refinement description - Version 1.2: 2024-11-13
Changes: Structure summary
