7TAM | pdb_00007tam

HRas G12V in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb7TAM/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-12-21 Released: 2022-12-28
Deposition Author(s): Kouidmi, I., Maddalena, M., Laplante, S.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.201 (Depositor), 0.202 (DCC)
R-Value Work:
0.174 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

SI/II Pocket of Ras: An Opportunity for a Once "Undruggable" Target

Franca, T.C.C., Maddalena, M., Kouidmi, I., Ayotte, Y., Islam, S.T., LaPlante, S.R.

(2025) ACS Omega

DOI: https://doi.org/10.1021/acsomega.4c10493

Macromolecule Content

Total Structure Weight: 19.45 kDa
Atom Count: 1,559
Modeled Residue Count: 166
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	A	166	Homo sapiens	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01112
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP 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]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.201 (Depositor), 0.202 (DCC)
R-Value Work: 0.174 (Depositor), 0.173 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.35	α = 90
b = 92.35	β = 90
c = 120.58	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MxDC	data collection
autoPROC	data processing
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	Canada	CQDM SynergiQC grant

Revision History (Full details and data files)

Version 1.0: 2022-12-28
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2025-03-12
Changes: Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.