3PLS | pdb_00003pls

RON in complex with ligand AMP-PNP

PDB DOI: https://doi.org/10.2210/pdb3PLS/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2010-11-15 Released: 2010-11-24
Deposition Author(s): Wang, J., Steinbacher, S., Augustin, M., Schreiner, P., Epstein, D., Mulvihill, M.J., Crew, A.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.290 (Depositor), 0.288 (DCC)
R-Value Work:
0.231 (Depositor), 0.236 (DCC)
R-Value Observed:
0.235 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of a Constitutively Active Mutant RON Kinase Suggests an Intramolecular Autophosphorylation Hypothesis

Wang, J., Steinbacher, S., Augustin, M., Schreiner, P., Epstein, D., Mulvihill, M.J., Crew, A.P.

(2010) Biochemistry 49: 7972-7974

PubMed: 20726546 Search on PubMed
DOI: https://doi.org/10.1021/bi100409w
Primary Citation Related Structures:
3PLS

PubMed Abstract:
A complex of RON(M1254T) with AMP-PNP and Mg(2+) reveals a substratelike positioning of Tyr1238 as well as likely catalysis-competent placement of the AMP-PNP and Mg(2+) components and indicates a tendency for cis phosphorylation. The structure shows how the oncogenic mutation may cause the constitutive activation and suggests a mechanistic hypothesis for the autophosphorylation of receptor tyrosine kinases.

Organizational Affiliation

OSI Pharmaceuticals, Inc., 1 Bioscience Park Drive, Farmingdale, New York 11735, USA. jwang@osip.com

Macromolecule Content

Total Structure Weight: 34.78 kDa
Atom Count: 2,509
Modeled Residue Count: 298
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage-stimulating protein receptor	A	298	Homo sapiens	Mutation(s): 1 Gene Names: MST1R, PTK8, RON EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q04912 (Homo sapiens) Explore Q04912 Go to UniProtKB: Q04912
PHAROS: Q04912 GTEx: ENSG00000164078
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04912
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP 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]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.290 (Depositor), 0.288 (DCC)
R-Value Work: 0.231 (Depositor), 0.236 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.631	α = 90
b = 98.631	β = 90
c = 45.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-11-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations