5WFN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

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

  • 4RWT - determined by Chen, X., Ni, F., Wang, Q.  

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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-5C
A, B
384Drosophila melanogasterMutations: E292K, K323P
Gene Names: Act5C
Find proteins for P10987 (Drosophila melanogaster)
Go to UniProtKB:  P10987
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Leiomodin-2
C, D
506Homo sapiensMutations: G439K, G442K, S440K, S446K, G445K, S443K, S438K, G437K
Gene Names: LMOD2
Find proteins for Q6P5Q4 (Homo sapiens)
Go to Gene View: LMOD2
Go to UniProtKB:  Q6P5Q4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 65.350α = 101.29
b = 65.650β = 90.94
c = 81.920γ = 107.97
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM073791
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM110352

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence
  • Version 1.2: 2018-01-31
    Type: Database references