3C5H

Crystal structure of the Ras homolog domain of human GRLF1 (p190RhoGAP)

PDB DOI: https://doi.org/10.2210/pdb3C5H/pdb

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

Deposited: 2008-01-31 Released: 2008-02-12
Deposition Author(s): Shen, L., Tong, Y., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.247 (Depositor), 0.260 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the Ras homolog domain of human GRLF1 (p190RhoGAP).

Shen, L., Tong, Y., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 29.52 kDa
Atom Count: 1,934
Modelled Residue Count: 232
Deposited Residue Count: 255
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor DNA-binding factor 1	A	255	Homo sapiens	Mutation(s): 0 Gene Names: GRLF1, GRF1, KIAA1722
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRY4 (Homo sapiens) Explore Q9NRY4 Go to UniProtKB: Q9NRY4
PHAROS: Q9NRY4 GTEx: ENSG00000160007
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NRY4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.247 (Depositor), 0.260 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.959	α = 90
b = 108.959	β = 90
c = 51.319	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MAR345	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-02-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations