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- PDB-6q9s: HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 14 AT 2.4A: Structura... -

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Basic information

Entry
Database: PDB / ID: 6q9s
TitleHDMX (14-111; C17S) COMPLEXED WITH COMPOUND 14 AT 2.4A: 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-HRN / 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: 2.4 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 1.2Oct 23, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Jan 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
C: Protein Mdm4
B: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,98327
Polymers33,5613
Non-polymers6,42224
Water63135
1
A: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1989
Polymers11,1871
Non-polymers2,0118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,06412
Polymers11,1871
Non-polymers2,87711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7206
Polymers11,1871
Non-polymers1,5335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.581, 93.581, 198.467
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-204-

SO4

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Components

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Protein , 1 types, 3 molecules ACB

#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.: 3 / 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, 59 molecules

#2: Chemical ChemComp-HRN / 3-[[6-chloranyl-3-[3-[(1~{S})-1-(2,4-dichlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]carbonylamino]-4-[4-(2-oxidanylidene-1,3-oxazinan-3-yl)piperidin-1-yl]benzoic acid


Mass: 812.139 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C42H37Cl3N6O5
#3: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C12H24O6
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.7 Å3/Da / Density % sol: 66.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.25M AmSO4, 6% 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: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2010
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.4→19.95 Å / Num. obs: 20849 / % possible obs: 99.6 % / Redundancy: 12.7 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.066 / Rrim(I) all: 0.064 / Net I/σ(I): 27.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 4.8 / Rpim(I) all: 0.445 / Rrim(I) all: 0.611 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q9Q

6q9q


Resolution: 2.4→19.95 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.825 / SU ML: 0.159 / SU R Cruickshank DPI: 0.3131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.235
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 1043 5 %RANDOM
Rwork0.2491 ---
obs0.25 19806 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 159.12 Å2 / Biso mean: 51.795 Å2 / Biso min: 32.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2.4→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 430 35 2547
Biso mean--62.07 53.85 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212564
X-RAY DIFFRACTIONr_angle_refined_deg1.32.1523394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.17524.94795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15815405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.366159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211745
LS refinement shellResolution: 2.4→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 73 -
Rwork0.315 1394 -
all-1467 -
obs--98.13 %

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