3Q3J

Crystal structure of plexin A2 RBD in complex with Rnd1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of plexin A2 RBD in complex with Rnd1

Wang, H.Tempel, W.Tong, Y.Guan, X.Shen, L.Buren, L.Zhang, N.Wernimont, A.K.Crombet, L.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Weigelt, J.Park, H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plexin-A2A112Homo sapiensMutation(s): 0 
Gene Names: PLXNA2KIAA0463OCTPLXN2UNQ209/PRO235
UniProt & NIH Common Fund Data Resources
Find proteins for O75051 (Homo sapiens)
Explore O75051 
Go to UniProtKB:  O75051
PHAROS:  O75051
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rho-related GTP-binding protein Rho6B214Homo sapiensMutation(s): 0 
Gene Names: RND1RHO6
UniProt & NIH Common Fund Data Resources
Find proteins for Q92730 (Homo sapiens)
Explore Q92730 
Go to UniProtKB:  Q92730
PHAROS:  Q92730
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
E [auth B]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , G [auth B] , H [auth B] , I [auth B] , J [auth B] , K [auth B] , L [auth B] , 
C [auth A],  D [auth A],  G [auth B],  H [auth B],  I [auth B],  J [auth B],  K [auth B],  L [auth B],  M [auth B]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.022α = 90
b = 67.129β = 90
c = 145.291γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description