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- PDB-4j7d: The 1.25A crystal structure of humanized Xenopus MDM2 with a nutl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j7d | ||||||
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Title | The 1.25A crystal structure of humanized Xenopus MDM2 with a nutlin fragment, RO5045331 | ||||||
![]() | E3 ubiquitin-protein ligase Mdm2 | ||||||
![]() | LIGASE/ANTAGONIST / PROTEIN-PROTEIN INTERACTION / E3 UBIQUITIN LIGASE / LIGASE-ANTAGONIST COMPLEX / P53 / IMIDAZOLINE / NUCLEUS | ||||||
Function / homology | ![]() regulation of biological quality / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / p53 binding / regulation of gene expression / regulation of cell cycle / protein ubiquitination / cell cycle / apoptotic process / nucleolus ...regulation of biological quality / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / p53 binding / regulation of gene expression / regulation of cell cycle / protein ubiquitination / cell cycle / apoptotic process / nucleolus / negative regulation of apoptotic process / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Janson, C. / Lukacs, C. / Graves, B. | ||||||
![]() | ![]() Title: Deconstruction of a nutlin: dissecting the binding determinants of a potent protein-protein interaction inhibitor. Authors: Fry, D.C. / Wartchow, C. / Graves, B. / Janson, C. / Lukacs, C. / Kammlott, U. / Belunis, C. / Palme, S. / Klein, C. / Vu, B. #1: ![]() Title: MDM2 small molecule antagonist RG7112 activates P53 signaling and regresses human tumors in preclinical cancer models Authors: Tovar, C. / Graves, B. / Packman, K. / Filipovic, Z. / Higgins, B. / Xia, M. / Tardell, C. / Garrido, R. / Lee, E. / Kolinsky, K. / To, K.-H. / Linn, M. / Podlaski, F. / Wovkulich, P. / Vu, B. / Vassilev, L.T. #2: ![]() Title: Discovery of RG7112: a small-molecule mdm2 antagonist in clinical development Authors: Vu, B. / Wovkulich, P. / Pizzolato, G. / Lovey, A. / Ding, Q. / Jiang, N. / Liu, J.-J. / Zhao, C. / Glenn, K. / Wen, Y. / Tovar, C. / Thompson, T. / Packman, K. / Vassilev, L. / Graves, B. #3: ![]() Title: In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Authors: Vassilev, L.T. / Vu, B.T. / Graves, B. / Carvajal, D. / Podlaski, F. / Filipovic, Z. / Kong, N. / Kammlott, U. / Lukacs, C. / Klein, C. / Fotouhi, N. / Liu, E.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.9 KB | Display | ![]() |
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PDB format | ![]() | 22.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.6 KB | Display | ![]() |
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Full document | ![]() | 774.8 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | N-TERMINAL FRAGMENT EXISTS AS A MONOMER BUT FULL-LENGTH PROTEIN WOULD BE A DIMER |
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Components
#1: Protein | Mass: 9962.615 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 21-105) / Mutation: I50L, P92H, L95I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P56273, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||
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#2: Chemical | ChemComp-I31 / ( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.18 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 40-50% SATURATED AMMONIUM SULFATE, 0.1M MES, PH 6.5, 5% PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.17→40 Å / Num. all: 28271 / Num. obs: 27483 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.4755 Å2 / ksol: 0.340739 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.25→34.51 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.25→1.33 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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