4NXR

Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Neurexin-1 Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions.

Liu, X.Speckhard, D.C.Shepherd, T.R.Sun, Y.J.Hengel, S.R.Yu, L.Fowler, C.A.Gakhar, L.Fuentes, E.J.

(2016) Structure 24: 2053-2066

  • DOI: https://doi.org/10.1016/j.str.2016.08.019
  • Primary Citation of Related Structures:  
    4NXP, 4NXQ, 4NXR

  • PubMed Abstract: 

    Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used the Tiam1 PDZ domain and an engineered variant (QM PDZ) with broadened specificity to investigate the role of structure and conformational dynamics in molecular recognition. Crystal structures of the QM PDZ domain both free and bound to ligands showed structural features central to binding (enthalpy), while nuclear-magnetic-resonance-based methyl relaxation experiments and isothermal titration calorimetry revealed that conformational entropy contributes to affinity. In addition to motions relevant to thermodynamics, slower microsecond to millisecond switching was prevalent in the QM PDZ ligand-binding site consistent with a role in ligand specificity. Our data indicate that conformational dynamics plays distinct and fundamental roles in tuning the affinity (conformational entropy) and specificity (excited-state conformations) of molecular interactions. More broadly, our results have important implications for the evolution, regulation, and design of protein-ligand interactions.


  • Organizational Affiliation

    Department of Chemistry, Loras College, Dubuque, IA 52004-0178, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-lymphoma invasion and metastasis-inducing protein 194Homo sapiensMutation(s): 5 
Gene Names: TIAM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13009 (Homo sapiens)
Explore Q13009 
Go to UniProtKB:  Q13009
GTEx:  ENSG00000156299 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13009
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neurexin-2-beta Peptide8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P58401 (Homo sapiens)
Explore P58401 
Go to UniProtKB:  P58401
GTEx:  ENSG00000110076 
Entity Groups  
UniProt GroupP58401
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANS
Query on ANS

Download Ideal Coordinates CCD File 
D [auth B]5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID)
C12 H13 N O3 S
BBEQQKBWUHCIOU-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
C [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.358α = 90
b = 50.323β = 90
c = 61.942γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references
  • Version 1.2: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-20
    Changes: Data collection, Refinement description