7C7J

Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Mechanistic Insights into the Interactions of Ras Subfamily GTPases with the SPN Domain of Autism-associated SHANK3.

Xu, X.L.Liu, J.P.Wang, Y.L.Wang, Y.Gong, X.Pan, L.F.

(2020) Chin J Chem 38: 1635-1641


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rap-1bA, B167Homo sapiensMutation(s): 2 
Gene Names: RAP1BOK/SW-cl.11
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61224 (Homo sapiens)
Explore P61224 
Go to UniProtKB:  P61224
PHAROS:  P61224
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SH3 and multiple ankyrin repeat domains protein 3C, D99Homo sapiensMutation(s): 0 
Gene Names: SHANK3KIAA1650PROSAP2PSAP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYB0 (Homo sapiens)
Explore Q9BYB0 
Go to UniProtKB:  Q9BYB0
PHAROS:  Q9BYB0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A], I [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.215α = 90
b = 191.926β = 90
c = 48.876γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-05-25 
  • Released Date: 2021-05-05 
  • Deposition Author(s): Xiao, L.X., Pan, L.F.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21822705

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release