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), 0.284 (DCC)
R-Value Work:
0.218 (Depositor), 0.215 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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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

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

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.277 (Depositor), 0.284 (DCC)
R-Value Work: 0.218 (Depositor), 0.215 (DCC)
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

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Ligand Structure Quality Assessment

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 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.