+Open data
-Basic information
Entry | Database: PDB / ID: 7rjf | |||||||||
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Title | MOPD-1 mutant-L47W | |||||||||
Components | [L47W]MOPD-1 | |||||||||
Keywords | ANTITUMOR PROTEIN / Synthetic peptide / disulfide-rich peptide / antitumor peptide / peptide mimetic | |||||||||
Function / homology | MALONATE ION Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Huawu, Y. / Conan, K.W. / Gordon, J.K. / Brett, M.C. / Yen-Hua, H. / David, J.C. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Rational Design of Potent Peptide Inhibitors of the PD-1:PD-L1 Interaction for Cancer Immunotherapy. Authors: Yin, H. / Zhou, X. / Huang, Y.H. / King, G.J. / Collins, B.M. / Gao, Y. / Craik, D.J. / Wang, C.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rjf.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rjf.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 7rjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rjf_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 7rjf_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 7rjf_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 7rjf_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/7rjf ftp://data.pdbj.org/pub/pdb/validation_reports/rj/7rjf | HTTPS FTP |
-Related structure data
Related structure data | 5jg9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5799.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.67 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 200 nL 5 mg/mL peptide + 200 nL 0.1 M zinc chloride, 8% v/v Tacsimate, pH 6.0, 16% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.47 Å / Num. obs: 10906 / % possible obs: 99.53 % / Redundancy: 2 % / Biso Wilson estimate: 28.89 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.55 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.231 / Num. unique obs: 1010 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5JG9 (scaffold) Resolution: 1.8→39.35 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.6433 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→39.35 Å
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Refine LS restraints |
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LS refinement shell |
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