9GHK | pdb_00009ghk

Crystal structure of Fyn SH3 domain/tau 214-220 peptide complex

PDB DOI: https://doi.org/10.2210/pdb9GHK/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-15 Released: 2025-08-27
Deposition Author(s): Becker, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.218 (Depositor), 0.217 (DCC)
R-Value Work:
0.178 (Depositor), 0.182 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Fyn SH3 domain/tau 214-220 peptide complex

Becker, S.

To be published.

Macromolecule Content

Total Structure Weight: 15.29 kDa
Atom Count: 1,170
Modeled Residue Count: 126
Deposited Residue Count: 138
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Tyrosine-protein kinase Fyn	A, B	64	Homo sapiens	Mutation(s): 0 Gene Names: FYN EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06241 (Homo sapiens) Explore P06241 Go to UniProtKB: P06241
PHAROS: P06241 GTEx: ENSG00000010810
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06241
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tau peptide ARG-THR-PRO-SER-LEU-PRO-THR-PRO-PRO-THR	C [auth Q]	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10636 (Homo sapiens) Explore P10636 Go to UniProtKB: P10636
PHAROS: P10636 GTEx: ENSG00000186868
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10636
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.218 (Depositor), 0.217 (DCC)
R-Value Work: 0.178 (Depositor), 0.182 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.631	α = 90
b = 54.163	β = 90
c = 66.868	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
pointless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-08-27
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.