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- PDB-1mcc: PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mcc | ||||||
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Title | PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS | ||||||
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![]() | IMMUNE SYSTEM / IMMUNOGLOBULIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Edmundson, A.B. / Harris, D.L. / Fan, Z.-C. / Guddat, L.W. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 64 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 384.4 KB | Display | ![]() |
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Full document | ![]() | 407.7 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mcbC ![]() 1mcdC ![]() 1mceC ![]() 1mcfC ![]() 1mchC ![]() 1mciC ![]() 1mcjC ![]() 1mckC ![]() 1mclC ![]() 1mcnC ![]() 1mcqC ![]() 1mcrC ![]() 1mcsC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 145 2: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION SER A 191 - HIS A 192 146.695 3: CIS PROLINE - PRO B 145 / 4: RESIDUE DPN P 2 IS A D FORM OF PHE 5: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION HIS P 3 - PRO P 4 246.36 6: RESIDUE DPN P 4 IS A D FORM OF PRO, ITS PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION HIS P 3 - PRO P 4 246.36 |
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Components
#1: Antibody | Mass: 22819.080 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #2: Protein/peptide | | Mass: 552.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Compound details | RESIDUE DPN P 2 IS THE D-PHE. RESIDUE DPN P 4 IS A D-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: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.47 % | ||||||||||||||||||||
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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: ![]() ![]() ![]() |
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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: 8625 |
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Processing
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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: 8625 / σ(F): 1.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |