8XND | pdb_00008xnd

Crystal structure of serine hydroxymethyltransferase 1

PDB DOI: https://doi.org/10.2210/pdb8XND/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-29 Released: 2025-04-02
Deposition Author(s): Fan, S., Wei, X., Lv, R., Wang, C., Tang, M., Jin, Y., Yang, Z.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free:
0.192 (Depositor), 0.167 (DCC)
R-Value Work:
0.153 (Depositor)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of serine hydroxymethyltransferase 1

Fan, S., Wei, X., Lv, R., Wang, C., Tang, M., Jin, Y., Yang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 207.82 kDa
Atom Count: 14,588
Modeled Residue Count: 1,888
Deposited Residue Count: 1,888
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, cytosolic	A, B, C, D	472	Homo sapiens	Mutation(s): 0 Gene Names: SHMT1 EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34896 (Homo sapiens) Explore P34896 Go to UniProtKB: P34896
PHAROS: P34896 GTEx: ENSG00000176974
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34896
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free: 0.192 (Depositor), 0.167 (DCC)
R-Value Work: 0.153 (Depositor)
R-Value Observed: 0.155 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.54	α = 90
b = 151.54	β = 90
c = 234.97	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		2018YFA0901800

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.