2VYP

Rabbit-muscle G-actin in complex with myxobacterial rhizopodin

• PDB DOI: https://doi.org/10.2210/pdb2VYP/pdb

• Classification: CONTRACTILE PROTEIN
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2008-07-25 Released: 2009-02-24 
• Deposition Author(s): Hagelueken, G., Albrecht, S.C., Steinmetz, H., Jansen, R., Heinz, D.W., Kalesse, M., Schubert, W.-D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.241 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

The Absolute Configuration of Rhizopodin and its Inhibition of Actin Polymerization by Dimerization.

Hagelueken, G., Albrecht, S.C., Steinmetz, H., Jansen, R., Heinz, D.W., Kalesse, M., Schubert, W.-D.

(2009) Angew Chem Int Ed Engl 48: 595

• PubMed: 19035596 
• DOI: https://doi.org/10.1002/anie.200802915
• Primary Citation of Related Structures:  
  2VYP

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Organizational Affiliation: 

Research Group Molecular Host-Pathogen Interactions, Helmholtz-Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 87.19 kDa 
• Atom Count: 5,844 
• Modelled Residue Count: 688 
• Deposited Residue Count: 754 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIN, ALPHA SKELETAL MUSCLE	A, B	377	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RH9	E [auth A]	RHIZOPODIN C78 H124 N4 O22 MWDPPGCTEBRUNT-IKBNIWNCSA-N
ATP	C [auth A], J [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
HEZ	F [auth A], G [auth A], H [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
CA	D [auth A], I [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.241 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.653	α = 90
b = 194.863	β = 90
c = 53.038	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Currently 2VYP does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2009-02-24 
Deposition Author(s): Hagelueken, G., Albrecht, S.C., Steinmetz, H., Jansen, R., Heinz, D.W., Kalesse, M., Schubert, W.-D.

Revision History  

• Version 1.0: 2009-02-24
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description