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

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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

Literature

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

Benova, V., Boura, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

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

Macromolecules

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 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

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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Benova, V., Boura, E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release