3EKU

Crystal Structure of Monomeric Actin bound to Cytochalasin D

Structural Biology Knowledgebase: 3EKU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EKU

Classification: CONTRACTILE PROTEIN

Total Structure Weight: 42921.98

Macromolecule Entities
Molecule Chains Length Organism Details
Actin-5C A 375 Drosophila melanogaster Mutation: A204E, P243K
Gene Name(s): Act5C CG4027
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CY9
Query on CY9

A (3S,3aR,4S,6S,6aR,7E,10S,12R,13E,15R,15aR)- 3-benzyl-6,12-dihydroxy-4,10,12-trimethyl- 5-methylidene-1,11-dioxo-2,3,3a,4,5,6,6a,9,10,11,12,15- dodecahydro-1H-cycloundeca[d]isoindol-15- yl acetate
Cytochalasin D (Synonym)
C30 H37 N O6
SDZRWUKZFQQKKV-JHADDHBZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ATP
Query on ATP

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.177
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 207.40 α = 90.00
b = 54.04 β = 98.96
c = 36.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-19
  • Released Date: 2008-10-07
  • Deposition author(s): Nair, U.B., Joel, P.B., Wan, Q., Lowey, S., Rould, M.A., Trybus, K.M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4