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- PDB-5uml: CRYSTAL STRUCTURE OF HUMAN MDMX IN COMPLEX WITH 12-MER PEPTIDE IN... -

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Basic information

Entry
Database: PDB / ID: 5uml
TitleCRYSTAL STRUCTURE OF HUMAN MDMX IN COMPLEX WITH 12-MER PEPTIDE INHIBITOR M3
Components
  • PEPTIDE INHIBITOR M3
  • Protein Mdm4
KeywordsCell Cycle / Antitumor Protein/Inhibitor / Oncoprotein / Antitumor Protein-Inhibitor complex
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / transcription repressor complex / DNA damage response, signal transduction by p53 class mediator / 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 / transcription repressor complex / DNA damage response, signal transduction by p53 class mediator / 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 / protein-containing complex assembly / Oxidative Stress Induced Senescence / cellular response to hypoxia / 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 / 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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPazgier, M. / Gohain, N. / Tolbert, W.D.
CitationJournal: To Be Published
Title: Design of ultrahigh-affinity and dual-specificity peptide antagonists of MDM2 and MDMX for p53 activation
Authors: Pazgier, M. / Gohain, N. / Tolbert, W.D.
History
DepositionJan 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Source and taxonomy
Category: pdbx_audit_support / pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Oct 21, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Oct 4, 2023Group: 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: PEPTIDE INHIBITOR M3
B: Protein Mdm4
D: PEPTIDE INHIBITOR M3
E: Protein Mdm4
F: PEPTIDE INHIBITOR M3
G: Protein Mdm4
H: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)44,4728
Polymers44,4728
Non-polymers00
Water00
1
A: Protein Mdm4
C: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)11,1182
Polymers11,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-13 kcal/mol
Surface area5660 Å2
MethodPISA
2
B: Protein Mdm4
D: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)11,1182
Polymers11,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-14 kcal/mol
Surface area5750 Å2
MethodPISA
3
E: Protein Mdm4
F: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)11,1182
Polymers11,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-15 kcal/mol
Surface area5550 Å2
MethodPISA
4
G: Protein Mdm4
H: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)11,1182
Polymers11,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-13 kcal/mol
Surface area5640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.413, 88.027, 46.300
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number4
Space group name H-MP1211

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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: 9575.293 Da / Num. of mol.: 4 / Fragment: residues 24-108 / Mutation: Q68A,Q69A,E70A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15151
#2: Protein/peptide
PEPTIDE INHIBITOR M3


Mass: 1542.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 14% (v/v) 2-Propanol ,70 mM Sodium acetate/ Hydrochloric acid pH 4.6, 140 mM Calcium chloride, 30% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 3592 / % possible obs: 49.8 % / Redundancy: 1.4 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.153 / Net I/σ(I): 2.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.364 / % possible all: 52.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RXZ

4rxz


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.788 / SU B: 96.288 / SU ML: 0.759 / Cross valid method: THROUGHOUT / ESU R Free: 1.152 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31526 180 5 %RANDOM
Rwork0.25791 ---
obs0.26079 3412 48.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å2-0 Å2-0.46 Å2
2--0.45 Å2-0 Å2
3----2.7 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 0 0 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193092
X-RAY DIFFRACTIONr_bond_other_d0.0030.022980
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9884170
X-RAY DIFFRACTIONr_angle_other_deg1.00536904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62624.154130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53615566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3191512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213334
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02606
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3413.4481504
X-RAY DIFFRACTIONr_mcbond_other0.343.4481503
X-RAY DIFFRACTIONr_mcangle_it0.6015.1681866
X-RAY DIFFRACTIONr_mcangle_other0.6015.1691867
X-RAY DIFFRACTIONr_scbond_it0.2363.4691588
X-RAY DIFFRACTIONr_scbond_other0.2363.4691589
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4335.22305
X-RAY DIFFRACTIONr_long_range_B_refined1.54263.93510930
X-RAY DIFFRACTIONr_long_range_B_other1.54263.93310930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 9 -
Rwork0.337 278 -
obs--51.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8542-0.86680.02351.41151.02962.8743-0.06550.26970.13590.02350.01440.04330.1906-0.10150.05120.0946-0.0118-0.00010.10340.04780.02560.4448-20.66243.0204
21.58661.53850.56216.21682.70461.18650.1431-0.0752-0.0060.0492-0.20030.0950.016-0.08580.05720.12250.03530.0080.08060.02090.1117-5.5831-26.873412.4006
30.3707-0.54440.57161.9467-0.4344.2117-0.09720.14760.07510.02120.073-0.1373-0.00730.22610.02410.0744-0.054-0.0130.14890.03070.0277-23.2234-3.98013.0274
43.08840.39553.0462.8529-1.603911.3012-0.2147-0.07990.3182-0.0419-0.13860.07-0.3851-0.14580.35330.07860.02610.00070.0743-0.03860.131-17.08532.041613.5188
52.0671-0.36231.39550.7776-0.67593.6018-0.05090.03090.1547-0.02810.03630.11970.06630.26160.01450.0893-0.0081-0.03190.051-0.00990.07932.0073-0.962426.2136
62.9582-2.04032.89741.6302-1.31465.1662-0.1105-0.1898-0.0620.07810.1130.07990.0501-0.3297-0.00260.1284-0.0006-0.03720.1337-0.00610.1962-4.73524.808436.6648
72.5150.7628-0.64960.3118-0.70993.7297-0.14110.0791-0.0729-0.01670.0792-0.0459-0.0248-0.29420.06190.09120.05910.00580.0781-0.01410.1201-25.2071-23.62826.2208
80.2507-0.65760.35531.7513-0.74555.5586-0.0836-0.0102-0.06670.0349-0.04960.1845-0.1833-0.26170.13320.1280.0378-0.00440.20490.01590.2003-18.6474-29.363936.4819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 108
2X-RAY DIFFRACTION2C2 - 11
3X-RAY DIFFRACTION3B25 - 108
4X-RAY DIFFRACTION4D1 - 11
5X-RAY DIFFRACTION5E26 - 108
6X-RAY DIFFRACTION6F1 - 11
7X-RAY DIFFRACTION7G26 - 108
8X-RAY DIFFRACTION8H1 - 11

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