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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/anie.200907002
Primary Citation of Related Structures:
3L8Y, 3L8Z

Organizational Affiliation

Universität Regensburg, Institut für Biophysik und Physikalische Biochemie, Universitätsstrasse 31, 93053 Regensburg, Germany.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01112
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
YCN Query on YCN Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,4,7,10-tetraazacyclododecane C₈ H₂₀ N₄ QBPPRVHXOZRESW-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-01-05

Deposition Author(s):

Revision History (Full details and data files)

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

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Deposit Data

Help and Resources

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Complex of Ras with cyclen

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations