4PR9

Human Vinculin (residues 891-1066) in complex with PIP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Mechanism and function of lipid-directed oligomerization of vinculin

Chinthalapudi, K.Rangarajan, E.S.Patil, D.Izard, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vinculin
A, B, C, D, E, F
A, B, C, D, E, F
176Homo sapiensMutation(s): 1 
Gene Names: VCL
UniProt & NIH Common Fund Data Resources
Find proteins for P18206 (Homo sapiens)
Explore P18206 
Go to UniProtKB:  P18206
PHAROS:  P18206
GTEx:  ENSG00000035403 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18206
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PIO
Query on PIO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
K [auth E]
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth B],
J [auth C],
L [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 32 1 2
  • Diffraction Data DOI: 10.15785/SBGRID/560 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.579α = 90
b = 102.579β = 90
c = 190.772γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
BUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
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: 2014-12-10
    Type: Initial release