3Q3J | pdb_00003q3j

Crystal structure of plexin A2 RBD in complex with Rnd1

• PDB DOI: https://doi.org/10.2210/pdb3Q3J/pdb

• Classification: Membrane protein/protein binding
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-12-21 Released: 2011-01-12 
• Deposition Author(s): 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., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.248 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Models: experimental

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.64 kDa 
• Atom Count: 2,153 
• Modeled Residue Count: 277 
• Deposited Residue Count: 326 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plexin-A2	A	112	Homo sapiens	Mutation(s): 0  Gene Names: PLXNA2, KIAA0463, OCT, PLXN2, UNQ209/PRO235
UniProt & NIH Common Fund Data Resources
Find proteins for O75051 (Homo sapiens) Explore O75051  Go to UniProtKB:  O75051
PHAROS:  O75051 GTEx:  ENSG00000076356

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho-related GTP-binding protein Rho6	B	214	Homo sapiens	Mutation(s): 0  Gene Names: RND1, RHO6
UniProt & NIH Common Fund Data Resources
Find proteins for Q92730 (Homo sapiens) Explore Q92730  Go to UniProtKB:  Q92730
PHAROS:  Q92730 GTEx:  ENSG00000172602

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.248 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.022	α = 90
b = 67.129	β = 90
c = 145.291	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-12 
Deposition Author(s): 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., Structural Genomics Consortium (SGC)

Revision History  

• 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
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description