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- PDB-1mcb: PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS -

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Basic information

Entry
Database: PDB / ID: 1mcb
TitlePRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS
Components
  • IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
  • PEPTIDE N-ACETYL-L-GLN-D-PHE-L-HIS-D-PRO-OH
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsEdmundson, 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
DepositionFeb 25, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 11, 2013Group: Database references / Source and taxonomy
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
B: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
P: PEPTIDE N-ACETYL-L-GLN-D-PHE-L-HIS-D-PRO-OH


Theoretical massNumber of molelcules
Total (without water)46,1933
Polymers46,1933
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-32 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.300, 72.300, 185.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: PEPTIDE BOND BETWEEN GLN A 6 AND PRO A 7 DEVIATE SIGNIFICANTLY FROM TRANS CONFORMATION ( 137.36 DEGREES)
2: CIS PROLINE - PRO A 145 / 3: CIS PROLINE - PRO B 145
4: RESIDUES PHE P 2 AND PRO P 4 ARE D FORMS OF THE AMINO ACIDS PEPTIDE BOND BETWEEN HIS P 3 AND PRO P 4 DEVIATE SIGNIFICANTLY FROM TRANS CONFORMATION ( 248.52 DEGREES)

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Components

#1: Antibody IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)


Mass: 22819.080 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6PIK1
#2: Protein/peptide PEPTIDE N-ACETYL-L-GLN-D-PHE-L-HIS-D-PRO-OH


Mass: 554.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
Sequence detailsTHE LIGHT CHAIN WAS SEQUENCED BY FETT AND DEUTSCH (1974) BIOCHEMISTRY, 13, 4102-4114.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growDetails: THIS COMPLEX WAS PREPARED BY COCRYSTALLIZATION WITH THE PEPTIDE.
Crystal grow
*PLUS
pH: 6.2 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Msodium pshosphate11
223 mg/mlprotein11
31.6-1.9 Mammonium sulfate11

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Wavelength: 1 Å
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.7→6 Å / σ(F): 1.5 /
RfactorNum. reflection
obs0.204 11140
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 0 0 3251
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.025
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0110.025
X-RAY DIFFRACTIONp_chiral_restr0.1220.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.5
X-RAY DIFFRACTIONp_multtor_nbd0.2570.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2020.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor8.18.1
X-RAY DIFFRACTIONp_staggered_tor24.724.7
X-RAY DIFFRACTIONp_orthonormal_tor22.322.3
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 6 Å / σ(F): 1.5 / Rfactor obs: 0.204 / Num. reflection obs: 11140
Solvent computation
*PLUS
Displacement parameters
*PLUS

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