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.
6TGH
SHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as external aldimine and as non-covalent complex
- PDB DOI: https://doi.org/10.2210/pdb6TGH/pdb
- Classification: TRANSFERASE
- Organism(s): Streptococcus thermophilus
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2019-11-15 Released: 2020-06-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.12 ?
- R-Value Free: 0.284
- R-Value Work: 0.237
- R-Value Observed: 0.239
Starting Model: experimental
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This is version 1.1 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], C [auth B], D | 415 | 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 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EVM (Subject of Investigation/LOI) Query on EVM | 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 | 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 | H [auth C], L [auth D] | D-SERINE C3 H7 N O3 MTCFGRXMJLQNBG-UWTATZPHSA-N |  | ||
| NA (Subject of Investigation/LOI) Query on NA | 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 ?
- R-Value Free: 0.284
- R-Value Work: 0.237
- R-Value Observed: 0.239
- Space Group: C 1 2 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 200.795 | ¦Á = 90 |
| b = 112.93 | ¦Â = 93.1 |
| c = 131.918 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| iMOSFLM | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2020-06-03 Deposition Author(s): Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.
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
