7S48 | pdb_00007s48

PAK4cat in complex with Integrin beta5 760-770 peptide

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-09-08 Released: 2022-11-09 
  • Deposition Author(s): Ha, B.H., Boggon, T.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7S48

This is version 1.3 of the entry. See complete history. 

Literature

Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4)

Ha, B.H., Yigit, S., Natarajan, N., Morse, E.M., Calderwood, D.A., Boggon, T.J.

(2022) Commun Biol 5: 1257

Macromolecule Content 

  • Total Structure Weight: 40.48 kDa 
  • Atom Count: 2,492 
  • Modeled Residue Count: 297 
  • Deposited Residue Count: 357 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 4346Homo sapiensMutation(s): 0 
Gene Names: PAK4, KIAA1142
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens)
Explore O96013 
Go to UniProtKB:  O96013
PHAROS:  O96013
GTEx:  ENSG00000130669 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96013
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin beta-511Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P18084 (Homo sapiens)
Explore P18084 
Go to UniProtKB:  P18084
PHAROS:  P18084
GTEx:  ENSG00000082781 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18084
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.735α = 90
b = 61.735β = 90
c = 179.987γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM138411

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary