8XNA | pdb_00008xna

Crystal structure of serine hydroxymethyltransferase 2

PDB DOI: https://doi.org/10.2210/pdb8XNA/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., Lv, R., Wang, C., Tang, M., Wei, X., Jin, Y., Yang, Z.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.198 (Depositor), 0.204 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of serine hydroxymethyltransferase 2

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

To be published.

Macromolecule Content

Total Structure Weight: 112.59 kDa
Atom Count: 7,269
Modeled Residue Count: 925
Deposited Residue Count: 1,008
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, mitochondrial	A, B	504	Homo sapiens	Mutation(s): 0 Gene Names: SHMT2 EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34897 (Homo sapiens) Explore P34897 Go to UniProtKB: P34897
PHAROS: P34897 GTEx: ENSG00000182199
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P34897
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.264 (Depositor), 0.264 (DCC)
R-Value Work: 0.198 (Depositor), 0.204 (DCC)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.605	α = 90
b = 160.605	β = 90
c = 210.404	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	2018YFA0901800

Revision History (Full details and data files)

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

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.