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- PDB-6q9l: HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Struc... -

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Basic information

Entry
Database: PDB / ID: 6q9l
TitleHDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
ComponentsE3 ubiquitin-protein ligase Mdm2
KeywordsLIGASE / PPI with p53 / inhibitor complex / cell cycle
Function / homology
Function and homology information


cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / response to ether / traversing start control point of mitotic cell cycle / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / fibroblast activation / Trafficking of AMPA receptors / receptor serine/threonine kinase binding ...cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / response to ether / traversing start control point of mitotic cell cycle / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / fibroblast activation / Trafficking of AMPA receptors / receptor serine/threonine kinase binding / peroxisome proliferator activated receptor binding / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of vascular associated smooth muscle cell migration / negative regulation of protein processing / SUMO transferase activity / response to steroid hormone / NEDD8 ligase activity / AKT phosphorylates targets in the cytosol / response to iron ion / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / positive regulation of muscle cell differentiation / cardiac septum morphogenesis / SUMOylation of ubiquitinylation proteins / regulation of postsynaptic neurotransmitter receptor internalization / blood vessel development / ligase activity / cellular response to alkaloid / Constitutive Signaling by AKT1 E17K in Cancer / regulation of protein catabolic process / negative regulation of signal transduction by p53 class mediator / negative regulation of DNA damage response, signal transduction by p53 class mediator / SUMOylation of transcription factors / response to magnesium ion / cellular response to UV-C / protein sumoylation / cellular response to actinomycin D / blood vessel remodeling / cellular response to estrogen stimulus / protein localization to nucleus / ribonucleoprotein complex binding / protein autoubiquitination / positive regulation of vascular associated smooth muscle cell proliferation / NPAS4 regulates expression of target genes / transcription repressor complex / positive regulation of mitotic cell cycle / regulation of heart rate / proteolysis involved in protein catabolic process / positive regulation of protein export from nucleus / ubiquitin binding / response to cocaine / DNA damage response, signal transduction by p53 class mediator / Stabilization of p53 / establishment of protein localization / Regulation of RUNX3 expression and activity / cellular response to gamma radiation / Oncogene Induced Senescence / protein destabilization / RING-type E3 ubiquitin transferase / Regulation of TP53 Activity through Methylation / cellular response to growth factor stimulus / response to toxic substance / centriolar satellite / cellular response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / disordered domain specific binding / p53 binding / endocytic vesicle membrane / ubiquitin protein ligase activity / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron projection development / 5S rRNA binding / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of cell cycle / Ub-specific processing proteases / postsynaptic density / protein ubiquitination / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / apoptotic process / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / glutamatergic synapse / enzyme binding
Similarity search - Function
E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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 ...E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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-HTZ / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 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: E3 ubiquitin-protein ligase Mdm2
B: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,91512
Polymers22,3122
Non-polymers1,60310
Water4,792266
1
A: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9225
Polymers11,1561
Non-polymers7664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9937
Polymers11,1561
Non-polymers8376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.773, 87.407, 37.141
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53- ...Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2


Mass: 11156.052 Da / Num. of mol.: 2 / Fragment: N-terminal domain, p53 binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-HTZ / [6-chloranyl-3-[3-[[4-chloranyl-2-(hydroxymethyl)phenyl]methyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]-[(3~{S})-3-[3-(dimethylamino)propyl-methyl-amino]pyrrolidin-1-yl]methanone


Mass: 659.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H40Cl2N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.7M AmSO4, 0.2M NaI, 0.2M NaCl, 0.2M TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97848 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2007
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 1.13→20 Å / Num. obs: 63421 / % possible obs: 91.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.065 / Χ2: 1.056 / Net I/σ(I): 12.1
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 3.05 / Num. unique obs: 6856 / Χ2: 2.048 / % possible all: 70.5

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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: 4DIJ

4dij


Resolution: 1.13→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.929 / SU ML: 0.021 / SU R Cruickshank DPI: 0.0438 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 3262 5.1 %RANDOM
Rwork0.1782 ---
obs0.1788 60546 91.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 42.72 Å2 / Biso mean: 11.377 Å2 / Biso min: 3.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 1.13→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 100 266 1914
Biso mean--7.23 20.69 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221680
X-RAY DIFFRACTIONr_angle_refined_deg1.5852.062276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2955186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.69324.11868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80115308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.987158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021230
X-RAY DIFFRACTIONr_nbd_refined0.2120.2713
X-RAY DIFFRACTIONr_nbtor_refined0.320.21162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2162
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.230
X-RAY DIFFRACTIONr_rigid_bond_restr1.47431817
X-RAY DIFFRACTIONr_sphericity_free7.0673274
X-RAY DIFFRACTIONr_sphericity_bonded6.45131640
LS refinement shellResolution: 1.132→1.161 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 164 -
Rwork0.184 3180 -
all-3344 -
obs--66.52 %

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