2REX

Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase.

Tong, Y.Tempel, W.Shen, L.Arrowsmith, C.H.Edwards, A.M.Sundstrom, M.Weigelt, J.Bochkarev, A.Park, H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plexin-B1A, C121Homo sapiensMutation(s): 0 
Gene Names: PLXNB1KIAA0407PLXN5SEP
UniProt & NIH Common Fund Data Resources
Find proteins for O43157 (Homo sapiens)
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Go to UniProtKB:  O43157
PHAROS:  O43157
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 Rho6B, D197Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
DA [auth D], K [auth B]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth D], J [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Download Ideal Coordinates CCD File 
AA [auth C] , E [auth A] , EA [auth D] , F [auth A] , FA [auth D] , G [auth A] , GA [auth D] , H [auth A] , 
AA [auth C],  E [auth A],  EA [auth D],  F [auth A],  FA [auth D],  G [auth A],  GA [auth D],  H [auth A],  HA [auth D],  IA [auth D],  JA [auth D],  KA [auth D],  L [auth B],  LA [auth D],  M [auth B],  MA [auth D],  N [auth B],  NA [auth D],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth C],  X [auth C],  Y [auth C],  Z [auth C]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.136α = 90
b = 71.653β = 128.36
c = 101.885γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data 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: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description