3H6N

Crystal Structure of the ubiquitin-like domain of plexin D1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.004 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plexin-D1
A
127Homo sapiensMutation(s): 0 
Gene Names: PLXND1 (KIAA0620)
Find proteins for Q9Y4D7 (Homo sapiens)
Go to Gene View: PLXND1
Go to UniProtKB:  Q9Y4D7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARS
Query on ARS

Download SDF File 
Download CCD File 
A
ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.004 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.777α = 90.00
b = 27.051β = 114.06
c = 52.653γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DMphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SHELXphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description