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Yorodumi- PDB-1mcd: PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mcd | |||||||||
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Title | PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS | |||||||||
Components |
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Keywords | IMMUNOGLOBULIN | |||||||||
Function / homology | Function and homology information immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON | |||||||||
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 | 1mcd.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mcd.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/1mcd ftp://data.pdbj.org/pub/pdb/validation_reports/mc/1mcd | HTTPS FTP |
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-Related structure data
Related structure data | 1mcbC 1mccC 1mceC 1mcfC 1mchC 1mciC 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: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION PRO A 1 - SER A 2 212.50 2: CIS PROLINE - PRO A 145 3: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION LYS A 167 - PRO A 168 211.66 4: CIS PROLINE - PRO B 145 5: RESIDUES PHE P 1 AND PRO P 4 ARE D FORMS OF THE AMINO ACIDS 6: RESIDUE BAL P 2 IS THE BETA FORM OF ALANINE. |
-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: UniProt: P0DOX8 #2: Protein/peptide | | Mass: 495.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) Sequence details | THE LIGHT CHAIN WAS SEQUENCED BY FETT AND DEUTSCH (1974) BIOCHEMIST | |
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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: 59.52 % | ||||||||||||||||||||
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Crystal grow | Details: THIS COMPLEX WAS PREPARED BY DIFFUSION OF THE PEPTIDE INTO 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 |
-Processing
Software |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 11140 / σ(F): 1.5 / Rfactor obs: 0.19 | ||||||||||
Solvent computation | *PLUS | ||||||||||
Displacement parameters | *PLUS |