7S48 | pdb_00007s48

PAK4cat in complex with Integrin beta5 760-770 peptide

PDB DOI: https://doi.org/10.2210/pdb7S48/pdb

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), 0.230 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

DOI: https://doi.org/10.1038/s42003-022-04157-3

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 4	A	346	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O96013
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-5	B	11	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18084
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.222 (Depositor), 0.230 (DCC)
R-Value Work: 0.179 (Depositor), 0.190 (DCC)
R-Value Observed: 0.182 (Depositor)

Diffraction Data: https://doi.org/10.15785/SBGRID/853

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.735	α = 90
b = 61.735	β = 90
c = 179.987	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM138411

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

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.