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), 0.230 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

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

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	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 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]