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- PDB-9fql: Crystal structure of hDM2 in complex with a peptidic ligand conta... -

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Basic information

Entry
Database: PDB / ID: 9fql
TitleCrystal structure of hDM2 in complex with a peptidic ligand containing a di-urea insert.
Components
  • E3 ubiquitin-protein ligase Mdm2
  • p25Lp26A
KeywordsANTITUMOR PROTEIN / PROTEIN FOLDAMER COMPLEX / PROTEIN FOLDAMER INTERACTIONS / PROTEIN PROTEIN INTERACTION INHIBITOR / UREA BASED CHIMERA FOLDAMER
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 / fibroblast activation / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / 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 / fibroblast activation / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / 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 / response to iron ion / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / regulation of postsynaptic neurotransmitter receptor internalization / cardiac septum morphogenesis / 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 / response to magnesium ion / SUMOylation of transcription factors / protein sumoylation / cellular response to UV-C / 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 / Stabilization of p53 / ubiquitin binding / positive regulation of protein export from nucleus / Regulation of RUNX3 expression and activity / response to cocaine / Oncogene Induced Senescence / DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / establishment of protein localization / cellular response to gamma radiation / protein destabilization / RING-type E3 ubiquitin transferase / cellular response to growth factor stimulus / response to toxic substance / centriolar satellite / endocytic vesicle membrane / cellular response to hydrogen peroxide / Signaling by ALK fusions and activated point mutants / protein polyubiquitination / Regulation of TP53 Degradation / ubiquitin-protein transferase activity / disordered domain specific binding / ubiquitin protein ligase activity / p53 binding / 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 / Regulation of TP53 Activity through Phosphorylation / cellular response to hypoxia / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / protein ubiquitination / regulation of cell cycle / postsynaptic density / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / ubiquitin protein ligase binding / apoptotic process / 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 / 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. ...E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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
Similarity search - Domain/homology
PHOSPHATE ION / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBuratto, J. / Mauran, L. / Goudreau, S. / Guichard, G.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Crystal structure of hDM2 in complex with a peptidic ligand containing a di-urea insert.
Authors: Buratto, J. / Mauran, L. / Goudreau, S. / Guichard, G.
History
DepositionJun 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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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
C: p25Lp26A
D: p25Lp26A
E: E3 ubiquitin-protein ligase Mdm2
F: E3 ubiquitin-protein ligase Mdm2
G: p25Lp26A
H: p25Lp26A
I: E3 ubiquitin-protein ligase Mdm2
J: E3 ubiquitin-protein ligase Mdm2
K: p25Lp26A
L: p25Lp26A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,52622
Polymers68,57712
Non-polymers95010
Water3,045169
1
A: E3 ubiquitin-protein ligase Mdm2
B: E3 ubiquitin-protein ligase Mdm2
C: p25Lp26A
D: p25Lp26A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3349
Polymers22,8594
Non-polymers4755
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-60 kcal/mol
Surface area9120 Å2
MethodPISA
2
E: E3 ubiquitin-protein ligase Mdm2
F: E3 ubiquitin-protein ligase Mdm2
G: p25Lp26A
H: p25Lp26A


Theoretical massNumber of molelcules
Total (without water)22,8594
Polymers22,8594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-28 kcal/mol
Surface area9150 Å2
MethodPISA
3
I: E3 ubiquitin-protein ligase Mdm2
K: p25Lp26A
hetero molecules

J: E3 ubiquitin-protein ligase Mdm2
L: p25Lp26A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3349
Polymers22,8594
Non-polymers4755
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area5000 Å2
ΔGint-57 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.986, 85.076, 198.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 26 and (name N or name...
21(chain B and ((resid 26 and (name N or name...
31(chain E and ((resid 26 and (name N or name...
41(chain F and ((resid 26 and (name N or name...
51(chain I and ((resid 26 and (name N or name...
61(chain J and (resid 26 through 28 or resid 30...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain A and ((resid 26 and (name N or name...AA262
12GLUGLUVALVAL(chain A and ((resid 26 and (name N or name...AA25 - 1101 - 86
13GLUGLUVALVAL(chain A and ((resid 26 and (name N or name...AA25 - 1101 - 86
14GLUGLUVALVAL(chain A and ((resid 26 and (name N or name...AA25 - 1101 - 86
15GLUGLUVALVAL(chain A and ((resid 26 and (name N or name...AA25 - 1101 - 86
21THRTHRTHRTHR(chain B and ((resid 26 and (name N or name...BB262
22THRTHRVALVAL(chain B and ((resid 26 and (name N or name...BB26 - 1102 - 86
23THRTHRVALVAL(chain B and ((resid 26 and (name N or name...BB26 - 1102 - 86
24THRTHRVALVAL(chain B and ((resid 26 and (name N or name...BB26 - 1102 - 86
25THRTHRVALVAL(chain B and ((resid 26 and (name N or name...BB26 - 1102 - 86
31THRTHRTHRTHR(chain E and ((resid 26 and (name N or name...EE262
32THRTHRVALVAL(chain E and ((resid 26 and (name N or name...EE26 - 1102 - 86
33THRTHRVALVAL(chain E and ((resid 26 and (name N or name...EE26 - 1102 - 86
34THRTHRVALVAL(chain E and ((resid 26 and (name N or name...EE26 - 1102 - 86
35THRTHRVALVAL(chain E and ((resid 26 and (name N or name...EE26 - 1102 - 86
41THRTHRTHRTHR(chain F and ((resid 26 and (name N or name...FF262
42GLUGLUVALVAL(chain F and ((resid 26 and (name N or name...FF25 - 1101 - 86
43GLUGLUVALVAL(chain F and ((resid 26 and (name N or name...FF25 - 1101 - 86
44GLUGLUVALVAL(chain F and ((resid 26 and (name N or name...FF25 - 1101 - 86
45GLUGLUVALVAL(chain F and ((resid 26 and (name N or name...FF25 - 1101 - 86
51THRTHRTHRTHR(chain I and ((resid 26 and (name N or name...II262
52GLUGLUVALVAL(chain I and ((resid 26 and (name N or name...II25 - 1101 - 86
53GLUGLUVALVAL(chain I and ((resid 26 and (name N or name...II25 - 1101 - 86
54GLUGLUVALVAL(chain I and ((resid 26 and (name N or name...II25 - 1101 - 86
55GLUGLUVALVAL(chain I and ((resid 26 and (name N or name...II25 - 1101 - 86
61THRTHRVALVAL(chain J and (resid 26 through 28 or resid 30...JJ26 - 282 - 4
62PROPROPROPRO(chain J and (resid 26 through 28 or resid 30...JJ30 - 326 - 8
63LEULEULEULEU(chain J and (resid 26 through 28 or resid 30...JJ33 - 359 - 11
64THRTHRVALVAL(chain J and (resid 26 through 28 or resid 30...JJ26 - 1102 - 86
65THRTHRVALVAL(chain J and (resid 26 through 28 or resid 30...JJ26 - 1102 - 86
66THRTHRVALVAL(chain J and (resid 26 through 28 or resid 30...JJ26 - 1102 - 86
67THRTHRVALVAL(chain J and (resid 26 through 28 or resid 30...JJ26 - 1102 - 86

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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: 10115.966 Da / Num. of mol.: 6 / Fragment: residues 17-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase
#2: Protein/peptide
p25Lp26A


Mass: 1313.456 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.58 Å3/Da / Density meas: 47.98 Mg/m3 / Density % sol: 52.4 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5 / Details: 1 M Na2HPO4/K2HPO4 pH 6.9, 30% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→42.85 Å / Num. obs: 49185 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 34.88 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.029 / Rrim(I) all: 0.102 / Net I/σ(I): 14.6 / Num. measured all: 619745 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0513.50.7294767635300.940.2040.7573.3100
8.94-42.859.70.0664326620.9980.0210.06429.199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
PHENIX1.13refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.651 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 2454 5 %
Rwork0.2206 46611 -
obs0.222 49065 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.83 Å2 / Biso mean: 48.6021 Å2 / Biso min: 16.76 Å2
Refinement stepCycle: final / Resolution: 2→37.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 50 169 4755
Biso mean--80.8 50.68 -
Num. residues----576
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1959X-RAY DIFFRACTION12.906TORSIONAL
12B1959X-RAY DIFFRACTION12.906TORSIONAL
13E1959X-RAY DIFFRACTION12.906TORSIONAL
14F1959X-RAY DIFFRACTION12.906TORSIONAL
15I1959X-RAY DIFFRACTION12.906TORSIONAL
16J1959X-RAY DIFFRACTION12.906TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.03850.32711310.2632491100
2.0385-2.08010.26271360.25682565100
2.0801-2.12530.32861340.25192541100
2.1253-2.17470.2741340.2372542100
2.1747-2.22910.29411350.24482568100
2.2291-2.28940.26741340.22572536100
2.2894-2.35670.27191350.22562581100
2.3567-2.43280.26031350.22052567100
2.4328-2.51970.24821350.22012547100
2.5197-2.62060.24311370.22492606100
2.6206-2.73980.28131340.23822553100
2.7398-2.88420.24521350.21842568100
2.8842-3.06480.25721380.21732616100
3.0648-3.30140.25511370.21352606100
3.3014-3.63330.20191370.2012608100
3.6333-4.15850.25021390.20182640100
4.1585-5.23710.21631410.1962681100
5.2371-37.6510.25521470.2563279599
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)
10.94230.05540.3530.8075-0.34551.30730.00370.039-0.0417-0.36240.0683-0.0720.14360.23310.01040.39280.01070.00060.2161-0.00540.212522.3198-27.92196.2001
20.75940.47020.73051.8891.09330.88580.0265-0.08560.02080.01720.012-0.21250.0839-0.070800.17630.01810.00240.2176-0.0030.206527.176-20.051628.176
30.0918-0.0108-0.06460.27680.19060.2366-0.0227-0.23240.1521-0.6929-0.24210.4896-0.4219-0.52880.0040.20090.0178-0.03990.27370.01580.243117.3983-24.010621.7324
40.0941-0.08270.03610.14220.0370.0524-0.08890.09510.4777-0.4804-0.20840.0864-0.28630.23-00.38920.02680.01060.2811-0.02220.289323.5036-16.878311.7945
50.8774-0.2613-0.0710.37740.3120.07980.40540.09750.1384-0.6102-0.3164-0.1652-0.3316-0.04980.08860.9711-0.0482-0.02880.56510.11380.54744.635514.10035.4646
6-0.0538-0.23630.08831.1390.61220.50180.03220.00310.4257-0.04530.2708-0.5614-0.0986-0.53560.11860.6181-0.08340.03390.7050.11310.68486.61321.517227.7751
70.00230.0046-0.02240.0171-0.00130.0529-0.15810.39980.2061-0.2271-0.22130.38490.0494-0.3234-0.00010.6492-0.0592-0.07571.12120.2540.6583-1.703716.663521.0357
80.0320.05580.06220.40090.11770.17120.5644-0.39960.2782-0.49780.2352-0.6413-0.148-0.0940.00371.16-0.18340.22080.69630.05240.6346.139124.978812.2347
91.6104-0.08211.14570.51090.27331.8213-0.02390.2879-0.0741-0.11540.02220.06190.05130.24580.0010.2023-0.00440.01240.2727-0.02350.25125.4772-3.848638.8033
100.69450.07520.50461.0349-0.65562.10090.0486-0.0891-0.06430.2283-0.0859-0.22310.15910.2038-0.00220.19920.0051-0.0050.2248-0.04590.2833-25.2663-3.817359.7918
110.04040.019-0.01130.05040.02520.0771-0.24080.26580.2742-0.1410.1147-0.358-0.35310.55670.00050.2295-0.0540.00940.3668-0.05750.340815.62181.254343.7663
120.0714-0.0402-0.03690.0465-0.01440.0883-0.16370.29440.6875-0.32660.07790.4607-0.5659-0.291200.28340.0263-0.01170.2579-0.06290.3291-34.90212.156754.3916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 25 through 110)A25 - 110
2X-RAY DIFFRACTION2(chain 'B' and resid 26 through 110)B26 - 110
3X-RAY DIFFRACTION3(chain 'C' and resid 17 through 27)C17 - 27
4X-RAY DIFFRACTION4(chain 'D' and resid 17 through 27)D17 - 27
5X-RAY DIFFRACTION5(chain 'E' and resid 26 through 110)E26 - 110
6X-RAY DIFFRACTION6(chain 'F' and resid 25 through 110)F25 - 110
7X-RAY DIFFRACTION7(chain 'G' and resid 17 through 27)G17 - 27
8X-RAY DIFFRACTION8(chain 'H' and resid 17 through 25)H17 - 25
9X-RAY DIFFRACTION9(chain 'I' and resid 25 through 111)I25 - 111
10X-RAY DIFFRACTION10(chain 'J' and resid 26 through 110)J26 - 110
11X-RAY DIFFRACTION11(chain 'K' and resid 17 through 27)K17 - 27
12X-RAY DIFFRACTION12(chain 'L' and resid 17 through 27)L17 - 27

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