4KLZ | pdb_00004klz

Inhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach applied to Rit1, a Target for Rheumatoid Arthritis

PDB DOI: https://doi.org/10.2210/pdb4KLZ/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-07 Released: 2014-09-17
Deposition Author(s): Shah, D.M., Kobayashi, M., Keizers, P.H., Tuin, A.W., Ab, E., Manning, L., Rzepiela, A.A., Andrews, M., Hoedemaeker, F.J., Siegal, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.311 (Depositor), 0.309 (DCC)
R-Value Work:
0.185 (Depositor), 0.192 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Inhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach applied to Rit1, a Target for Rheumatoid Arthritis

Shah, D.M., Kobayashi, M., Keizers, P.H., Tuin, A.W., Ab, E., Manning, L., Rzepiela, A.A., Andrews, M., Hoedemaeker, F.J., Siegal, G.

To be published.

Macromolecule Content

Total Structure Weight: 20.55 kDa
Atom Count: 1,336
Modeled Residue Count: 156
Deposited Residue Count: 173
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein Rit1	A	173	Homo sapiens	Mutation(s): 0 Gene Names: RIT1, RIBB, RIT, ROC1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92963 (Homo sapiens) Explore Q92963 Go to UniProtKB: Q92963
PHAROS: Q92963 GTEx: ENSG00000143622
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92963
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 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]
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: 2.30 Å
R-Value Free: 0.311 (Depositor), 0.309 (DCC)
R-Value Work: 0.185 (Depositor), 0.192 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.278	α = 90
b = 37.048	β = 95.9
c = 40.736	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
Coot	model building
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description