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

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Basic information

Entry
Database: PDB / ID: 1mcj
TitlePRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS
Components
  • IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
  • PEPTIDE N-ACETYL-D-PHE-L-HIS-D-PRO-NH2
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETYL GROUP / D-PHENYLALANINE / D-PROLINE / AMINO GROUP / :
Function and homology information
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 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-D-PHE-L-HIS-D-PRO-NH2
A: ACETYL GROUP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4037
Polymers46,0633
Non-polymers3404
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-31 kcal/mol
Surface area19020 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: CIS PROLINE - PRO A 145 / 2: CIS PROLINE - PRO A 168 / 3: CIS PROLINE - PRO B 145
4: RESIDUES PHE P 1 AND PRO P 3 ARE D FORMS OF THE AMINO ACIDS

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Components

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Antibody / Protein/peptide , 2 types, 3 molecules ABP

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


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 PEPTIDE N-ACETYL-D-PHE-L-HIS-D-PRO-NH2


Mass: 424.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

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Non-polymers , 4 types, 4 molecules A

#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-DPN / D-PHENYLALANINE


Type: D-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical ChemComp-DPR / D-PROLINE


Type: D-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2

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Details

Has protein modificationY
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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growDetails: 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
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
obs0.193 6738
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 22 0 3242
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.025
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.03
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_restr0.010.025
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.1920.5
X-RAY DIFFRACTIONp_multtor_nbd0.2680.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1920.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor88
X-RAY DIFFRACTIONp_staggered_tor25.925.9
X-RAY DIFFRACTIONp_orthonormal_tor33.133.1
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 6783 / σ(F): 1.5 / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS

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