1MCF

PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Principles and pitfalls in designing site-directed peptide ligands.

Edmundson, A.B.Harris, D.L.Fan, Z.C.Guddat, L.W.Schley, B.T.Hanson, B.L.Tribbick, G.Geysen, H.M.

(1993) Proteins 16: 246-267

  • DOI: 10.1002/prot.340160304
  • Primary Citation of Related Structures:  1MCB, 1MCC, 1MCD, 1MCE, 1MCH, 1MCI, 1MCJ, 1MCK, 1MCL, 1MCN, 1MCQ, 1MCR, 1MCS

  • PubMed Abstract: 
  • An immunoglobulin light chain dimer with a large generic binding cavity was used as a host molecule for designing a series of peptide guest ligands. In a screening procedure peptides coupled to solid supports were systematically tested for binding ac ...

    An immunoglobulin light chain dimer with a large generic binding cavity was used as a host molecule for designing a series of peptide guest ligands. In a screening procedure peptides coupled to solid supports were systematically tested for binding activity by enzyme linked immunosorbent assays (ELISA). Key members of the binding series were synthesized in milligram quantities and diffused into crystals of the host molecule for X-ray analyses. These peptides were incrementally increased in size and affinity until they nearly filled the cavity. Progressive changes in binding patterns were mapped by comparisons of crystallographically refined structures of 14 peptide-protein complexes at 2.7 A resolution. These comparisons led to guidelines for ligand design and also suggested ways to modify previously established binding patterns. By manipulating equilibria involving histidine, for example, it was possible to abolish one important intramolecular interaction of the bound ligand and substitute another. These events triggered a change in conformation of the ligand from a compact to an extended form and a comprehensive change in the mode of binding to the protein. In dipeptides of histidine and proline, protonation of both imidazolium nitrogen atoms was used to program an end-to-end reversal of the direction in which the ligand was inserted into the binding cavity. Peptides cocrystallized with proteins produced complexes somewhat different in structure from those in which ligands were diffused into preexisting crystals. In such a large and malleable cavity, space utilization was thus different when a ligand was introduced before the imposition of crystal packing restraints.


    Related Citations: 
    • Binding of N-Formylated Chemotactic Peptides in Crystals of the Mcg Light Chain Dimer: Similarities with Neutrophil Receptors
      Edmundson, A.B.,Ely, K.R.
      (1985) Mol.Immunol. 22: 463
    • Binding of 2,4-Dinitrophenyl Compounds and Other Small Molecules to a Crystalline Lambdal-Type Bence-Jones Dimer
      Edmundson, A.B.,Ely, K.R.,Girling, R.L.,Abola, E.E.,Schiffer, M.,Westholm, F.A.,Fausch, M.D.,Deutsch, H.F.
      (1974) Biochemistry 13: 3816
    • A Search for Site-Filling Ligands in the Mcg Bence-Jones Dimer: Crystal Binding Studies of Fluorescent Compounds
      Edmundson, A.B.,Ely, K.R.,Herron, J.N.,Cheson, B.D.
      (1984) Mol.Immunol. 7: 561
    • The Binding of Opioid Peptides to the Mcg Light Chain Dimer: Flexible Keys and Adjustable Locks
      Edmundson, A.B.,Ely, K.R.,Herron, J.N.,Cheson, B.D.
      (1987) Mol.Immunol. 24: 915


    Organizational Affiliation

    Harrington Cancer Center, Amarillo, Texas 79106.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
A, B
216Homo sapiensGene Names: IGL@
Find proteins for Q6PIK1 (Homo sapiens)
Go to UniProtKB:  Q6PIK1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE N-ACETYL-L-GLN-D-PHE-L-HIS-D-PRO-B-ALA-B-ALA-OH
P
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DPR
Query on DPR

Download SDF File 
Download CCD File 
P
D-PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-SCSAIBSYSA-N
 Ligand Interaction
BAL
Query on BAL

Download SDF File 
Download CCD File 
P
BETA-ALANINE
C3 H7 N O2
UCMIRNVEIXFBKS-UHFFFAOYSA-N
 Ligand Interaction
DPN
Query on DPN

Download SDF File 
Download CCD File 
P
D-PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-MRVPVSSYSA-N
 Ligand Interaction
HIS
Query on HIS

Download SDF File 
Download CCD File 
P
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
ACE
Query on ACE

Download SDF File 
Download CCD File 
P
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
BAL
Query on BAL
P
peptide-likeC3 H7 N O2

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ACE
Query on ACE
P
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.300α = 90.00
b = 72.300β = 90.00
c = 185.900γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other