3WPS

crystal structure of the GAP domain of MgcRacGAP(S387D)

• PDB DOI: https://doi.org/10.2210/pdb3WPS/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2014-01-15 Released: 2015-01-21 
• Deposition Author(s): Murayama, K., Kato-murayama, M., Shirouzu, M., Kitamura, T., Yokoyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.259 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Starting Model: experimental

Literature

crystal structure of the GAP domain of MgcRacGAP

Murayama, K., Kato-Murayama, M., Shirouzu, M., Kitamura, T., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.48 kDa 
• Atom Count: 3,279 
• Modelled Residue Count: 402 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rac GTPase-activating protein 1	A, B	208	Homo sapiens	Mutation(s): 1  Gene Names: RACGAP1, KIAA1478, MGCRACGAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0H5 (Homo sapiens) Explore Q9H0H5  Go to UniProtKB:  Q9H0H5
PHAROS:  Q9H0H5 GTEx:  ENSG00000161800

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.259 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.321	α = 90
b = 77.321	β = 90
c = 108.744	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Murayama, K., Kato-murayama, M., Shirouzu, M., Kitamura, T., Yokoyama, S.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-13
  Changes: Structure summary