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- PDB-1ttv: NMR Structure of a Complex Between MDM2 and a Small Molecule Inhibitor -

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Basic information

Entry
Database: PDB / ID: 1ttv
TitleNMR Structure of a Complex Between MDM2 and a Small Molecule Inhibitor
ComponentsUbiquitin-protein ligase E3 Mdm2
KeywordsLIGASE / MDM2 / protein-protein interaction
Function / homology
Function and homology information


regulation of biological quality / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / regulation of cell cycle / apoptotic process / nucleolus / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding ...regulation of biological quality / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / regulation of cell cycle / apoptotic process / nucleolus / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
MDM2 / SWIB/MDM2 domain / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others ...MDM2 / SWIB/MDM2 domain / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-IMY / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / simulated annealing
AuthorsFry, D.C. / Emerson, S.D. / Palme, S. / Vu, B.T. / Liu, C.M. / Podlaski, F.
CitationJournal: J.Biomol.Nmr / Year: 2004
Title: NMR structure of a complex between MDM2 and a small molecule inhibitor.
Authors: Fry, D.C. / Emerson, S.D. / Palme, S. / Vu, B.T. / Liu, C.M. / Podlaski, F.
History
DepositionJun 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN AUTHOR NOTED THAT THE piperizinyl moiety produced no NOEs, so the positions of its atoms ...HETEROGEN AUTHOR NOTED THAT THE piperizinyl moiety produced no NOEs, so the positions of its atoms could not be determined experimentally AND ARE NOT INCLUDED IN THE COORDINATES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-protein ligase E3 Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7742
Polymers12,2071
Non-polymers5681
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 42structures with acceptable covalent geometry,structures with the least restraint violations
RepresentativeModel #4fewest violations

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Components

#1: Protein Ubiquitin-protein ligase E3 Mdm2 / p53-binding protein Mdm2 / Double minute 2 protein / Xdm2


Mass: 12206.883 Da / Num. of mol.: 1 / Fragment: resiudes 13-119 / Mutation: I50L, P92H, L95I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: MDM2 / Plasmid: pUBS 520 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P56273, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-IMY / 1-{[4,5-BIS(4-CHLOROPHENYL)-2-(2-ISOPROPOXY-4-METHOXYPHENYL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]CARBONYL}PIPERAZINE / CIS-[4,5-BIS-(4-CHLOROPHENYL)-2-(2-ISOPROPOXY-4-METHOXYPHENYL)-4,5-DIHYD ROIMIDAZOL-1-YL]-PIPERAZIN-1-YL-METHANONE


Mass: 567.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H32Cl2N4O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D 13C/15N-filtered NOESY

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Sample preparation

DetailsContents: 0.6mM 13C/15N-MDM2; 3.5mM inhibitor; 50mM d13-MES; 150mM KCl; 50mM d10-DTT; 1.5mM NaN3
Solvent system: 92% H2O, 8% D2O
Sample conditionsIonic strength: 50mM d13-MES; 150mM KCl; 50mM d10-DTT; 1.5mM NaN3
pH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000Hare et al.processing
NMRView5.0.3Johnson and Blevinsdata analysis
CNX2000.1Brunger et al.structure solution
CNX2000.1Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure calculations utilized 1169 NOE-based distance constraints, of which 54 were intermolecular; 176 dihedral angle constraints; and 48 hydrogen bond constraints. The piperazinyl moiety ...Details: Structure calculations utilized 1169 NOE-based distance constraints, of which 54 were intermolecular; 176 dihedral angle constraints; and 48 hydrogen bond constraints. The piperazinyl moiety of the inhibitor gave no NOEs, hence the positions of its atoms are not known and the stereochemistry is not rigorously established.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations
Conformers calculated total number: 42 / Conformers submitted total number: 18

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