9F6S | pdb_00009f6s

PDZ domain in complex with the peptide from AP2-associated protein kinase 1

PDB DOI: https://doi.org/10.2210/pdb9F6S/pdb

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

Deposited: 2024-05-02 Released: 2025-05-14
Deposition Author(s): Benova, V., Boura, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

PDZ domain in complex with the peptide from AP2-associated protein kinase 1

Benova, V., Boura, E.

To be published.

Macromolecule Content

Total Structure Weight: 10.07 kDa
Atom Count: 806
Modeled Residue Count: 90
Deposited Residue Count: 96
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PDZ and LIM domain protein 5	A	90	Homo sapiens	Mutation(s): 0 Gene Names: PDLIM5, ENH, L9
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HC4 (Homo sapiens) Explore Q96HC4 Go to UniProtKB: Q96HC4
PHAROS: Q96HC4 GTEx: ENSG00000163110
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96HC4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AP2-associated protein kinase 1	B	6	Homo sapiens	Mutation(s): 0 Gene Names: AAK1, KIAA1048 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q2M2I8 (Homo sapiens) Explore Q2M2I8 Go to UniProtKB: Q2M2I8
PHAROS: Q2M2I8 GTEx: ENSG00000115977
Entity Groups
UniProt Group	Q2M2I8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.213 (Depositor), 0.214 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.93	α = 90
b = 37.84	β = 90
c = 52.39	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
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.