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- PDB-6q9q: HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 13 AT 2.1A; Structura... -

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Basic information

Entry
Database: PDB / ID: 6q9q
TitleHDMX (14-111; C17S) COMPLEXED WITH COMPOUND 13 AT 2.1A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
ComponentsProtein Mdm4
KeywordsAPOPTOSIS / HDMX / MDM4
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / ventricular septum development / transcription repressor complex / DNA damage response, signal transduction by p53 class mediator / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / ventricular septum development / transcription repressor complex / DNA damage response, signal transduction by p53 class mediator / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process / Regulation of TP53 Activity through Methylation / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / protein-containing complex assembly / Oxidative Stress Induced Senescence / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / Ub-specific processing proteases / protein stabilization / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / 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 superfamily / Zinc finger RanBP2-type signature. / 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-HUE / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Protein Mdm4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKallen, J.
CitationJournal: Chemmedchem / Year: 2019
Title: Structural States of Hdm2 and HdmX: X-ray Elucidation of Adaptations and Binding Interactions for Different Chemical Compound Classes.
Authors: Kallen, J. / Izaac, A. / Chau, S. / Wirth, E. / Schoepfer, J. / Mah, R. / Schlapbach, A. / Stutz, S. / Vaupel, A. / Guagnano, V. / Masuya, K. / Stachyra, T.M. / Salem, B. / Chene, P. / ...Authors: Kallen, J. / Izaac, A. / Chau, S. / Wirth, E. / Schoepfer, J. / Mah, R. / Schlapbach, A. / Stutz, S. / Vaupel, A. / Guagnano, V. / Masuya, K. / Stachyra, T.M. / Salem, B. / Chene, P. / Gessier, F. / Holzer, P. / Furet, P.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Mdm4
B: Protein Mdm4
C: Protein Mdm4
D: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,41720
Polymers44,7484
Non-polymers4,66916
Water2,702150
1
A: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2174
Polymers11,1871
Non-polymers1,0303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5736
Polymers11,1871
Non-polymers1,3865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2174
Polymers11,1871
Non-polymers1,0303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4096
Polymers11,1871
Non-polymers1,2225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.801, 75.367, 62.773
Angle α, β, γ (deg.)90.000, 93.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 11186.985 Da / Num. of mol.: 4 / Fragment: N-terminal domain, p53 binding domain / Mutation: C17S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O15151

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Non-polymers , 5 types, 166 molecules

#2: Chemical
ChemComp-HUE / 6-chloranyl-3-[3-[(1~{S})-1-(4-chlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-~{N}-[2-(4-cyclohexylpiperazin-1-yl)ethyl]-1~{H}-indole-2-carboxamide


Mass: 669.686 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H42Cl2N6O
#3: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H24O6
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.14 Å3/Da / Density % sol: 60.77 % / Mosaicity: 0.347 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.6M AmSO4, 4% w/v 18-crown-ether, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2009
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 31374 / % possible obs: 97.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.036 / Χ2: 0.994 / Net I/σ(I): 34.15 / Num. measured all: 130733
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.92 / Num. unique obs: 3071 / Χ2: 1.498 / % possible all: 96.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FE7

3fe7


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.583 / SU ML: 0.123 / SU R Cruickshank DPI: 0.2162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.177
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 1583 5 %RANDOM
Rwork0.234 ---
obs0.2349 29783 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.5 Å2 / Biso mean: 47.738 Å2 / Biso min: 29.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.42 Å2
2--2.36 Å20 Å2
3----2.6 Å2
Refinement stepCycle: final / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 314 150 3149
Biso mean--53.59 57.61 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223068
X-RAY DIFFRACTIONr_angle_refined_deg1.0492.0974113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3685331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.11724.839124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25315523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4491512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212184
LS refinement shellResolution: 2.103→2.157 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 103 -
Rwork0.278 2077 -
all-2180 -
obs--92.81 %

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