3L8Y | pdb_00003l8y

Complex of Ras with cyclen

• PDB DOI: https://doi.org/10.2210/pdb3L8Y/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-04 Released: 2011-01-05 
• Deposition Author(s): Rosnizeck, I.C., Graf, T., Spoerner, M., Traenkle, J., Filchtinski, D., Herrmann, C., Gremer, L., Vetter, I.R., Wittinghofer, A., Koenig, B., Kalbitzer, H.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Stabilizing a weak binding state for effectors in the human ras protein by cyclen complexes

Rosnizeck, I.C., Graf, T., Spoerner, M., Trankle, J., Filchtinski, D., Herrmann, C., Gremer, L., Vetter, I.R., Wittinghofer, A., Konig, B., Kalbitzer, H.R.

(2010) Angew Chem Int Ed Engl 49: 3830-3833

• PubMed: 20401883 
• DOI: https://doi.org/10.1002/anie.200907002
• Primary Citation Related Structures: 
  3L8Y, 3L8Z

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Organizational Affiliation: 
• Universität Regensburg, Institut für Biophysik und Physikalische Biochemie, Universitätsstrasse 31, 93053 Regensburg, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 19.82 kDa 
• Atom Count: 1,526 
• Modeled Residue Count: 166 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	A	166	Homo sapiens	Mutation(s): 0  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112 GTEx:  ENSG00000174775

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
YCN	H [auth A]	1,4,7,10-tetraazacyclododecane C8 H20 N4 QBPPRVHXOZRESW-UHFFFAOYSA-N
ZN	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88	α = 90
b = 88	β = 90
c = 134	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-05 
Deposition Author(s): Rosnizeck, I.C., Graf, T., Spoerner, M., Traenkle, J., Filchtinski, D., Herrmann, C., Gremer, L., Vetter, I.R., Wittinghofer, A., Koenig, B., Kalbitzer, H.R.

Revision History  

• Version 1.0: 2011-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description