5WFN

Revised model of leiomodin 2-mediated actin regulation (alternate refinement of PDB 4RWT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ANPClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4RWT


Literature

Crystal structure of leiomodin 2 in complex with actin: a structural and functional reexamination

Boczkowska, M.Yurtsever, Z.Rebowski, G.Eck, M.J.Dominguez, R.

(2017) Biophys J 113: 889-899


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-5CA,
C [auth B]
384Drosophila melanogasterMutation(s): 2 
Gene Names: Act5CCG4027
EC: 3.6.4
UniProt
Find proteins for P10987 (Drosophila melanogaster)
Explore P10987 
Go to UniProtKB:  P10987
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10987
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Leiomodin-2B [auth C],
D
506Homo sapiensMutation(s): 8 
Gene Names: LMOD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P5Q4 (Homo sapiens)
Explore Q6P5Q4 
Go to UniProtKB:  Q6P5Q4
PHAROS:  Q6P5Q4
GTEx:  ENSG00000170807 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P5Q4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.35α = 101.29
b = 65.65β = 90.94
c = 81.92γ = 107.97
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ANPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM073791
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM110352

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2018-01-31
    Changes: Database references
  • Version 1.3: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2020-09-23
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-03-13
    Changes: Data collection, Database references