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- PDB-3jzq: Human MDMX liganded with a 12mer peptide inhibitor (pDIQ) -

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Basic information

Entry
Database: PDB / ID: 3jzq
TitleHuman MDMX liganded with a 12mer peptide inhibitor (pDIQ)
Components
  • Protein Mdm4
  • pDIQ peptide (12mer)
KeywordsCELL CYCLE / P53-BINDING PROTEIN MDM4 / DOUBLE MINUTE 4 PROTEIN / Alternative splicing / Metal-binding / Nucleus / Polymorphism / Zinc / Zinc-finger
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / negative regulation of protein catabolic process / Oncogene Induced Senescence ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / negative regulation of protein catabolic process / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / cellular response to hypoxia / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
MDM4 / : / MDM2 / SWIB/MDM2 domain / 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 ...MDM4 / : / MDM2 / SWIB/MDM2 domain / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchonbrunn, E. / Phan, J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure-based design of high affinity peptides inhibiting the interaction of p53 with MDM2 and MDMX.
Authors: Phan, J. / Li, Z. / Kasprzak, A. / Li, B. / Sebti, S. / Guida, W. / Schonbrunn, E. / Chen, J.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Mdm4
P: pDIQ peptide (12mer)
B: Protein Mdm4
Q: pDIQ peptide (12mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5455
Polymers23,4494
Non-polymers961
Water2,504139
1
A: Protein Mdm4
P: pDIQ peptide (12mer)


Theoretical massNumber of molelcules
Total (without water)11,7252
Polymers11,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-12 kcal/mol
Surface area5830 Å2
MethodPISA
2
B: Protein Mdm4
Q: pDIQ peptide (12mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8213
Polymers11,7252
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-26 kcal/mol
Surface area5900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.925, 53.735, 87.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein Mdm4 / p53-binding protein Mdm4 / Mdm2-like p53-binding protein / Protein Mdmx / Double minute 4 protein


Mass: 10160.899 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Plasmid: pDEST-His-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) pLysS / References: UniProt: O15151
#2: Protein/peptide pDIQ peptide (12mer)


Mass: 1563.687 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2.1 M ammonium sulfate, 10 mM Tris HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 20193 / Num. obs: 20193 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1953 / % possible all: 99

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Processing

Software
NameClassification
StructureStudiodata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3DAB

3dab


Resolution: 1.8→34.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 965 -random
Rwork0.208 ---
all0.208 19850 --
obs-19850 98.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 5 139 1735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.352 142 -
Rwork0.295 --
obs-2913 93.5 %

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