10ZB | pdb_000010zb

Room-temperature X-ray structure of E53Q mutant of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in complex with PLP-L-Ser external aldimine and tetrahydrofolate (THF)

PDB DOI: https://doi.org/10.2210/pdb10ZB/pdb

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

Deposited: 2026-02-12 Released: 2026-05-20
Deposition Author(s): Kovalevsky, A., Drago, V.N., Phillips, R.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.185 (Depositor), 0.184 (DCC)
R-Value Work:
0.158 (Depositor), 0.159 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study

Drago, V.N., Phillips, R.S., Kovalevsky, A.

(2026) RSC Adv 16: 22600-22609

DOI: https://doi.org/10.1039/D6RA01814A

Macromolecule Content

Total Structure Weight: 90.25 kDa
Atom Count: 6,760
Modeled Residue Count: 804
Deposited Residue Count: 810
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A	405	Thermus thermophilus	Mutation(s): 1 Gene Names: glyA, TthAA11_16450 EC: 2.1.2.1
UniProt
Find proteins for A0AAD1KUU5 (Thermus thermophilus) Explore A0AAD1KUU5 Go to UniProtKB: A0AAD1KUU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAD1KUU5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	B	405	Thermus thermophilus	Mutation(s): 1 Gene Names: glyA, TthAA11_16450 EC: 2.1.2.1
UniProt
Find proteins for A0AAD1KUU5 (Thermus thermophilus) Explore A0AAD1KUU5 Go to UniProtKB: A0AAD1KUU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAD1KUU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THG (Subject of Investigation/LOI) Query on THG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(6S)-5,6,7,8-TETRAHYDROFOLATE C₁₉ H₂₃ N₇ O₆ MSTNYGQPCMXVAQ-RYUDHWBXSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
KOU (Subject of Investigation/LOI) Query on KOU Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine C₁₁ H₁₅ N₂ O₈ P ZTQZHYMXYBDMIL-BIMOUXMDSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]