2C2H

CRYSTAL STRUCTURE OF THE HUMAN RAC3 IN COMPLEX WITH GDP

• PDB DOI: https://doi.org/10.2210/pdb2C2H/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-09-29 Released: 2005-10-13 
• Deposition Author(s): Debreczeni, J.E., Yang, X., Zao, Y., Elkins, J., Gileadi, C., Burgess, N., Colebrook, S., Gileadi, O., Fedorov, O., Bunkoczi, G., von Delft, F., Doyle, D., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.229 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Crystal Structure of the Human Rac3 in Complex with Gdp

Debreczeni, J.E., Yang, X., Zao, Y., Elkins, J., Gileadi, C., Burgess, N., Colebrook, S., Gileadi, O., Fedorov, O., Bunkoczi, G., von Delft, F., Doyle, D., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 47.7 kDa 
• Atom Count: 3,027 
• Modelled Residue Count: 341 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3	A, B	192	Homo sapiens	Mutation(s): 0  EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P60763 (Homo sapiens) Explore P60763  Go to UniProtKB:  P60763
PHAROS:  P60763 GTEx:  ENSG00000169750

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], S [auth B], T [auth B], U [auth B], V [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
SO4	BA [auth B], CA [auth B], M [auth A], N [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	AA [auth B], FA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], R [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	DA [auth B], EA [auth B], O [auth A], P [auth A], Q [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.229 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.32	α = 90
b = 110.32	β = 90
c = 81.79	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-13 
Deposition Author(s): Debreczeni, J.E., Yang, X., Zao, Y., Elkins, J., Gileadi, C., Burgess, N., Colebrook, S., Gileadi, O., Fedorov, O., Bunkoczi, G., von Delft, F., Doyle, D., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A.

Revision History  

• Version 1.0: 2005-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2018-02-28
  Changes: Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description