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- PDB-6q9y: HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 16 AT 1.20A; Structur... -

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Basic information

Entry
Database: PDB / ID: 6q9y
TitleHDMX (14-111; C17S) COMPLEXED WITH COMPOUND 16 AT 1.20A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
ComponentsProtein Mdm4
KeywordsAPOPTOSIS / HDMX / MDM4 / DIMER INDUCTION
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
Chem-HRQ / Protein Mdm4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,0734
Polymers22,3742
Non-polymers6992
Water3,189177
1
A: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5362
Polymers11,1871
Non-polymers3491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5362
Polymers11,1871
Non-polymers3491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.492, 42.426, 107.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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.: 2 / 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
#2: Chemical ChemComp-HRQ / 7-methoxy-~{N}-[(3~{S})-1-(4-methylphenyl)pyrrolidin-3-yl]-1~{H}-indole-3-carboxamide


Mass: 349.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2.5M AmSO4, 0.1M KSCN, 1% v/v MPD, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2013
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.2→19.73 Å / Num. obs: 60131 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.039 / Net I/σ(I): 25.7
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.871 / Rrim(I) all: 0.571 / % possible all: 99.2

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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: 1.2→19.73 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.902 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.039
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 3007 5 %RANDOM
Rwork0.1608 ---
obs0.162 57124 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.02 Å2 / Biso mean: 14.678 Å2 / Biso min: 6.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.2→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 52 177 1610
Biso mean--7.88 28.04 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221565
X-RAY DIFFRACTIONr_angle_refined_deg1.2682.0362131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.07925.22467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02315309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.53156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211174
X-RAY DIFFRACTIONr_rigid_bond_restr1.43631565
X-RAY DIFFRACTIONr_sphericity_free4.2423177
X-RAY DIFFRACTIONr_sphericity_bonded3.54631517
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 218 -
Rwork0.206 4132 -
all-4350 -
obs--99.22 %

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