2GF0

The crystal structure of the human DiRas1 GTPase in the inactive GDP bound state

PDB DOI: https://doi.org/10.2210/pdb2GF0/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-03-21 Released: 2006-04-04
Deposition Author(s): Turnbull, A.P., Papagrigoriou, E., Yang, X., Schoch, G., Elkins, J., Gileadi, O., Salah, E., Bray, J., Wen-Hwa, L., Fedorov, O., Niesen, F.E., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Doyle, D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.208
R-Value Work: 0.160
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of the human DiRas1 GTPase in the inactive GDP bound state

Turnbull, A.P., Papagrigoriou, E., Yang, X., Schoch, G., Elkins, J., Gileadi, O., Salah, E., Bray, J., Wen-Hwa, L., Fedorov, O., Niesen, F.E., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Doyle, D.

To be published.

Macromolecule Content

Total Structure Weight: 91.65 kDa
Atom Count: 6,183
Modelled Residue Count: 688
Deposited Residue Count: 796
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein Di-Ras1	A, B, C, D	199	Homo sapiens	Mutation(s): 0 Gene Names: DIRAS1, GBTS1, RIG
UniProt & NIH Common Fund Data Resources
Find proteins for O95057 (Homo sapiens) Explore O95057 Go to UniProtKB: O95057
PHAROS: O95057 GTEx: ENSG00000176490
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95057
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.208
R-Value Work: 0.160
R-Value Observed: 0.161
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.053	α = 90
b = 94.031	β = 89.98
c = 61.214	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-04-04

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-04-04
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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2GF0

The crystal structure of the human DiRas1 GTPase in the inactive GDP bound state

The crystal structure of the human DiRas1 GTPase in the inactive GDP bound state

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)