8TQF

Crystal structure of Soybean SHMT8 in complex with PLP-glycine and diglutamylated 5-formyltetrahydrofolate

PDB DOI: https://doi.org/10.2210/pdb8TQF/pdb

Classification: TRANSFERASE
Organism(s): Glycine max
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-07 Released: 2024-08-21
Deposition Author(s): Owuocha, L.F., Beamer, L.J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.214
R-Value Work: 0.184
R-Value Observed: 0.186

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

Structural insights into high affinity binding of polyglutamylated tetrahydrofolate to soybean serine hydroxymethyltransferase

Owuocha, L.F., Beamer, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 221.01 kDa
Atom Count: 16,518
Modelled Residue Count: 1,888
Deposited Residue Count: 1,968
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B, C, D	492	Glycine max	Mutation(s): 0 Gene Names: 100305380 EC: 2.1.2.1
UniProt
Find proteins for A0A0R0IK90 (Glycine max) Explore A0A0R0IK90 Go to UniProtKB: A0A0R0IK90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0R0IK90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S8R (Subject of Investigation/LOI) Query on S8R Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	H [auth A], M [auth B], T [auth C], Y [auth D]	N-[4-({[(6R)-2-amino-5-formyl-4-hydroxy-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-glutamic acid C₂₅ H₃₀ N₈ O₁₀ QZHOZGNCYBQAQZ-PMPSAXMXSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D]
PLG Query on PLG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain W [auth D]	E [auth A], L [auth B], P [auth C], W [auth D]	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] C₁₀ H₁₅ N₂ O₇ P FEVQWBMNLWUBTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain W [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth D]	F [auth A] G [auth A] I [auth A] J [auth A] K [auth A] F [auth A], G [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], X [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth D]