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

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Basic information

Entry
Database: PDB / ID: 1mcf
TitlePRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS
Components
  • Immunoglobulin lambda-1 light chain
  • PEPTIDE N-ACETYL-L-GLN-D-PHE-L-HIS-D-PRO-B-ALA-B-ALA-OH
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / 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 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin lambda-1 light chain / IGL@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
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: Non-polymer description / 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 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin lambda-1 light chain
B: Immunoglobulin lambda-1 light chain
P: PEPTIDE N-ACETYL-L-GLN-D-PHE-L-HIS-D-PRO-B-ALA-B-ALA-OH


Theoretical massNumber of molelcules
Total (without water)46,3353
Polymers46,3353
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-29 kcal/mol
Surface area18840 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 B 145
3: RESIDUES PHE D 2 AND PRO D 4 ARE D FORMS OF THE AMINO ACIDS
4: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION ALA P 5 - ALA P 6 222.079 RESIDUE BAL P 5 AND BAL P 6 ARE BETA FORMS OF ALANINE.

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Components

#1: Antibody Immunoglobulin lambda-1 light chain / Immunoglobulin lambda-1 light chain MCG


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, UniProt: Q6PIK1*PLUS
#2: Protein/peptide PEPTIDE N-ACETYL-L-GLN-D-PHE-L-HIS-D-PRO-B-ALA-B-ALA-OH


Mass: 696.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
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: 3.03 Å3/Da / Density % sol: 59.34 %
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
obs0.194 8554
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 42 0 3261
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.025
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0220.03
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_restr0.0090.025
X-RAY DIFFRACTIONp_chiral_restr0.1220.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.5
X-RAY DIFFRACTIONp_multtor_nbd0.2560.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2010.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor7.37.3
X-RAY DIFFRACTIONp_staggered_tor25.625.6
X-RAY DIFFRACTIONp_orthonormal_tor27.227.2
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 8554 / σ(F): 1.5 / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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