9DT9 | pdb_00009dt9

Crystal Structure of 231_C2_TrkA

PDB DOI: https://doi.org/10.2210/pdb9DT9/pdb

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

Deposited: 2024-09-30 Released: 2025-04-23
Deposition Author(s): Bera, A.K., Schlichthaerle, T., Kang, A., Baker, D.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.286 (Depositor), 0.284 (DCC)
R-Value Work:
0.226 (Depositor)
R-Value Observed:
0.232 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

De novo design of TrkA specific agonists

Schlichthaerle, T., Baker, D.

To be published.

Macromolecule Content

Total Structure Weight: 26.51 kDa
Atom Count: 1,925
Modeled Residue Count: 224
Deposited Residue Count: 232
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
231_C2_TrkA	A, B	116	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.286 (Depositor), 0.284 (DCC)
R-Value Work: 0.226 (Depositor)
R-Value Observed: 0.232 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.467	α = 90
b = 60.459	β = 94.09
c = 51.88	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-04-23
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.