12TD | pdb_000012td

Structure of de novo designed salen-binding enzyme

PDB DOI: https://doi.org/10.2210/pdb12TD/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-04-17 Released: 2026-04-29
Deposition Author(s): Bakanas, I., Horst, M., DeGrado, W.F.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.259 (Depositor), 0.258 (DCC)
R-Value Work:
0.214 (Depositor), 0.215 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 12TD

This is version 1.1 of the entry. See complete history.

Literature

De Novo Design of Catalytically Active Salen-Binding Proteins

Bakanas, I., Horst, M., DeGrado, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 31.87 kDa
Atom Count: 2,325
Modeled Residue Count: 288
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed salen-binding enzyme	A, B	146	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.259 (Depositor), 0.258 (DCC)
R-Value Work: 0.214 (Depositor), 0.215 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.792	α = 90
b = 86.449	β = 90
c = 81.545	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM122603
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM154484
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM163375
National Science Foundation (NSF, United States)	United States	2448848 MC2574
National Science Foundation (NSF, United States)	United States	2528384

Revision History (Full details and data files)

Version 1.0: 2026-04-29
Type: Initial release
Version 1.1: 2026-05-13
Changes: Derived calculations, Experimental preparation

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.