9DHB | pdb_00009dhb

STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE 5 FROM GLYCINE MAX CULTIVAR ESSEX COMPLEXED WITH PLP-GLYCINE AND 5-FORMYLTETRAHYDROFOLATE

PDB DOI: https://doi.org/10.2210/pdb9DHB/pdb

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

Deposited: 2024-09-03 Released: 2025-09-17
Deposition Author(s): Beamer, L.J., Owuocha, L.F.
Funding Organization(s): National Science Foundation (NSF, United States), National Institute of Food and Agriculture (NIFA, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.226 (Depositor), 0.223 (DCC)
R-Value Work:
0.176 (Depositor), 0.175 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE 5 FROM GLYCINE MAX CULTIVAR ESSEX COMPLEXED WITH PLP-GLYCINE AND 5-FORMYLTETRAHYDROFOLATE

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

To be published.

Macromolecule Content

Total Structure Weight: 222.07 kDa
Atom Count: 16,250
Modeled Residue Count: 1,884
Deposited Residue Count: 1,984
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	496	Glycine max	Mutation(s): 0 Gene Names: 100815417, GLYMA_05G152100 EC: 2.1.2.1
UniProt
Find proteins for A0A0R4J3C9 (Glycine max) Explore A0A0R4J3C9 Go to UniProtKB: A0A0R4J3C9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0R4J3C9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FFO (Subject of Investigation/LOI) Query on FFO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	F [auth A], J [auth B], N [auth C], Q [auth D]	N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid C₂₀ H₂₃ N₇ O₇ VVIAGPKUTFNRDU-STQMWFEESA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D]
PLG (Subject of Investigation/LOI) Query on PLG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	E [auth A], I [auth B], M [auth C], P [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 I [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] K [auth B] L [auth B] O [auth C] G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], R [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.226 (Depositor), 0.223 (DCC)
R-Value Work: 0.176 (Depositor), 0.175 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.732	α = 90
b = 131.883	β = 91.019
c = 117.412	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

Beamer, L.J.

Owuocha, L.F.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2152548
National Institute of Food and Agriculture (NIFA, United States)	United States	021-67013-35887