6YRW | pdb_00006yrw

SHMT from Streptococcus thermophilus Tyr55Ser variant as internal aldimine and as non-covalent complex with D-Ser

PDB DOI: https://doi.org/10.2210/pdb6YRW/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus thermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-04-20 Released: 2020-06-03
Deposition Author(s): Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.227 (Depositor), 0.228 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

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.

Macromolecule Content

Total Structure Weight: 181.84 kDa
Atom Count: 12,948
Modeled Residue Count: 1,640
Deposited Residue Count: 1,664
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B [auth C], C [auth B], D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M0B4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] SDF format, chain J [auth B] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D]	E [auth A], H [auth C], J [auth B], M [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Focus chain J [auth B] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth C] Focus chain J [auth B] Focus chain M [auth D]
DSN (Subject of Investigation/LOI) Query on DSN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] SDF format, chain K [auth B] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain K [auth B] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C] mmCIF format, chain K [auth B] mmCIF format, chain N [auth D]	F [auth A], I [auth C], K [auth B], N [auth D]	D-SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-UWTATZPHSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Focus chain K [auth B] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth C] Focus chain K [auth B] Focus chain N [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]