1F3M | pdb_00001f3m

CRYSTAL STRUCTURE OF HUMAN SERINE/THREONINE KINASE PAK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1F3M

This is version 1.4 of the entry. See complete history

Literature

Structure of PAK1 in an autoinhibited conformation reveals a multistage activation switch.

Lei, M.Lu, W.Meng, W.Parrini, M.C.Eck, M.J.Mayer, B.J.Harrison, S.C.

(2000) Cell 102: 387-397

  • DOI: https://doi.org/10.1016/s0092-8674(00)00043-x
  • Primary Citation Related Structures: 
    1F3M

  • PubMed Abstract: 

    The p21-activated kinases (PAKs), stimulated by binding with GTP-liganded forms of Cdc42 or Rac, modulate cytoskeletal actin assembly and activate MAP-kinase pathways. The 2.3 A resolution crystal structure of a complex between the N-terminal autoregulatory fragment and the C-terminal kinase domain of PAK1 shows that GTPase binding will trigger a series of conformational changes, beginning with disruption of a PAK1 dimer and ending with rearrangement of the kinase active site into a catalytically competent state. An inhibitory switch (IS) domain, which overlaps the GTPase binding region of PAK1, positions a polypeptide segment across the kinase cleft. GTPase binding will refold part of the IS domain and unfold the rest. A related switch has been seen in the Wiskott-Aldrich syndrome protein (WASP).


  • Organizational Affiliation
    • Laboratory of Molecular Medicine, Children's Hospital, Boston, Massachusetts 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 88.46 kDa 
  • Atom Count: 6,187 
  • Modeled Residue Count: 712 
  • Deposited Residue Count: 754 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE PAK-ALPHAA,
C [auth B]
80Homo sapiensMutation(s): 0 
EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13153 (Homo sapiens)
Explore Q13153 
Go to UniProtKB:  Q13153
PHAROS:  Q13153
GTEx:  ENSG00000149269 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13153
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE PAK-ALPHAB [auth C],
D
297Homo sapiensMutation(s): 0 
EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13153 (Homo sapiens)
Explore Q13153 
Go to UniProtKB:  Q13153
PHAROS:  Q13153
GTEx:  ENSG00000149269 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13153
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth C],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.583α = 90
b = 94.583β = 90
c = 147.497γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations