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Yorodumi- PDB-1mci: PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mci | ||||||
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Title | PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Edmundson, A.B. / Harris, D.L. / Fan, Z.-C. / Guddat, L.W. | ||||||
Citation | Journal: Proteins / Year: 1993 Title: Principles and pitfalls in designing site-directed peptide ligands. Authors: Edmundson, A.B. / Harris, D.L. / Fan, Z.C. / Guddat, L.W. / Schley, B.T. / Hanson, B.L. / Tribbick, G. / Geysen, H.M. #1: Journal: Mol.Immunol. / Year: 1987 Title: The Binding of Opioid Peptides to the Mcg Light Chain Dimer: Flexible Keys and Adjustable Locks Authors: Edmundson, A.B. / Ely, K.R. / Herron, J.N. / Cheson, B.D. #2: Journal: Mol.Immunol. / Year: 1985 Title: Binding of N-Formylated Chemotactic Peptides in Crystals of the Mcg Light Chain Dimer: Similarities with Neutrophil Receptors Authors: Edmundson, A.B. / Ely, K.R. #3: Journal: Mol.Immunol. / Year: 1984 Title: A Search for Site-Filling Ligands in the Mcg Bence-Jones Dimer: Crystal Binding Studies of Fluorescent Compounds Authors: Edmundson, A.B. / Ely, K.R. / Herron, J.N. / Cheson, B.D. #4: Journal: Biochemistry / Year: 1974 Title: Binding of 2,4-Dinitrophenyl Compounds and Other Small Molecules to a Crystalline Lambdal-Type Bence-Jones Dimer Authors: Edmundson, A.B. / Ely, K.R. / Girling, R.L. / Abola, E.E. / Schiffer, M. / Westholm, F.A. / Fausch, M.D. / Deutsch, H.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mci.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mci.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mci_validation.pdf.gz | 381.4 KB | Display | wwPDB validaton report |
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Full document | 1mci_full_validation.pdf.gz | 405.9 KB | Display | |
Data in XML | 1mci_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1mci_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/1mci ftp://data.pdbj.org/pub/pdb/validation_reports/mc/1mci | HTTPS FTP |
-Related structure data
Related structure data | 1mcbC 1mccC 1mcdC 1mceC 1mcfC 1mchC 1mcjC 1mckC 1mclC 1mcnC 1mcqC 1mcrC 1mcsC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 145 / 2: CIS PROLINE - PRO B 145 / 3: RESIDUE DPN P 1 IS THE D FORM OF PHE. / 4: RESIDUE DPR P 3 IS THE D FORM OF A CIS PROLINE. |
-Components
#1: Antibody | Mass: 22819.080 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: PIR: S14675 #2: Protein/peptide | | Mass: 426.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Compound details | RESIDUE DPN P 1 IS THE D-PHE. RESIDUE DPR P 3 IS THE D-CIS-PRO. | Sequence details | 1. THE FOLLOWING TABLE MAY BE USED TO RELATE THE ENTRIES SEQUENCE NUMBERING TO THE NUMBERING SYSTEM ...1. THE FOLLOWING TABLE MAY BE USED TO RELATE THE ENTRIES SEQUENCE NUMBERING TO THE NUMBERING SYSTEM OF E.KABAT (E.A.KABAT,T.T.WU,M.REID-MILLER,H.M.PERRY,K.S.GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % | ||||||||||||||||||||
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Crystal grow | Details: THIS COMPLEX WAS PREPARED BY DIFFUSION OF THE PEPTIDE INTO A CRYSTAL OF THE DIMER | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.2 / Method: batch method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Wavelength: 1 Å |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→15 Å / Num. obs: 6067 |
-Processing
Software |
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Refinement | Resolution: 2.7→6 Å / σ(F): 1.5 /
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Refinement step | Cycle: LAST / Resolution: 2.7→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 6067 / σ(F): 1.5 / Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |