9RWD | pdb_00009rwd

High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)

PDB DOI: https://doi.org/10.2210/pdb9RWD/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-07-09 Released: 2025-08-13
Deposition Author(s): Warlich, A., Ruszkowski, M., Nawrot, D.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.178 (Depositor), 0.178 (DCC)
R-Value Work:
0.145 (Depositor), 0.145 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9RWD

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

Literature

High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)

Warlich, A., Ruszkowski, M., Nawrot, D.

To be published.

Macromolecule Content

Total Structure Weight: 213.26 kDa
Atom Count: 16,539
Modeled Residue Count: 1,819
Deposited Residue Count: 1,904
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, mitochondrial	A, B, C, D	476	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34897
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain J [auth A]	AA [auth D], J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth D] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] L [auth B] E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C]	BA [auth D], K [auth A], Q [auth B], W [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain W [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.178 (Depositor), 0.178 (DCC)
R-Value Work: 0.145 (Depositor), 0.145 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.184	α = 90
b = 125.571	β = 93.675
c = 135.137	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2023/50/E/NZ7/00501

Revision History (Full details and data files)

Version 1.0: 2025-08-13
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.