9DAI | pdb_00009dai

Crystal structure of Trk-A in complex with Staurosporin

PDB DOI: https://doi.org/10.2210/pdb9DAI/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-08-22 Released: 2025-09-03
Deposition Author(s): Johnson, E., Greasley, S.E., Kraus, M.L., Cronin, C.N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free:
0.277 (Depositor), 0.295 (DCC)
R-Value Work:
0.218 (Depositor)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9DAI

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Trk-A in complex with Staurosporin

Johnson, E.

To be published.

Macromolecule Content

Total Structure Weight: 36.58 kDa
Atom Count: 2,145
Modeled Residue Count: 264
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A	320	Homo sapiens	Mutation(s): 0 Gene Names: NTRK1, MTC, TRK, TRKA EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens) Explore P04629 Go to UniProtKB: P04629
PHAROS: P04629 GTEx: ENSG00000198400
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STU (Subject of Investigation/LOI) Query on STU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	STAUROSPORINE C₂₈ H₂₆ N₄ O₃ HKSZLNNOFSGOKW-FYTWVXJKSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.277 (Depositor), 0.295 (DCC)
R-Value Work: 0.218 (Depositor)
R-Value Observed: 0.220 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.529	α = 90
b = 45.612	β = 127.06
c = 79.473	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
BUSTER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-09-03
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.