3H6N

Crystal Structure of the ubiquitin-like domain of plexin D1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.276 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the ubiquitin-like domain of plexin D1

Tong, Y.Nedyalkova, L.Tempel, W.MacKenzie, F.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Weigelt, J.Bochkarev, A.Buck, M.Park, H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plexin-D1127Homo sapiensMutation(s): 0 
Gene Names: PLXND1KIAA0620
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4D7 (Homo sapiens)
Explore Q9Y4D7 
Go to UniProtKB:  Q9Y4D7
PHAROS:  Q9Y4D7
GTEx:  ENSG00000004399 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4D7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.777α = 90
b = 27.051β = 114.06
c = 52.653γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary