22IT | pdb_000022it

Crystal structure of LbSCT1 in complex with Spermidine

PDB DOI: https://doi.org/10.2210/pdb22IT/pdb

Classification: TRANSFERASE
Organism(s): Lycium barbarum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-01-13 Released: 2026-01-28
Deposition Author(s): Wang, G.Q., Hu, D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: in silico
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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 and catalytic mechanistic insights into caffeoyltransferase underpin lycibarbarspermidine biosynthesis in Lycium barbarum

Li, S.Y., Wang, G.Q., Hu, D.

To be published.

Macromolecule Content

Total Structure Weight: 53.06 kDa
Atom Count: 3,658
Modeled Residue Count: 445
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caffeoyltransferase	A	470	Lycium barbarum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPD (Subject of Investigation/LOI) Query on SPD Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.256 (Depositor), 0.256 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.34	α = 90
b = 64.34	β = 90
c = 113.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-01-28
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.