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

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Basic information

Entry
Database: PDB / ID: 1mci
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-OH
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
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 1.4Nov 6, 2024Group: 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
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.pdbx_leaving_atom_flag / _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

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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-OH


Theoretical massNumber of molelcules
Total (without water)46,0653
Polymers46,0653
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-30 kcal/mol
Surface area19230 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: RESIDUE DPN P 1 IS THE D FORM OF PHE. / 4: RESIDUE DPR P 3 IS THE D FORM OF A CIS PROLINE.

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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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: PIR: S14675
#2: Protein/peptide PEPTIDE N-ACETYL-D-PHE-L-HIS-D-PRO-OH


Mass: 426.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Compound detailsRESIDUE DPN P 1 IS THE D-PHE. RESIDUE DPR P 3 IS THE D-CIS-PRO.
Has protein modificationY
Sequence details1. 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 IMMUNOLOGICAL INTEREST, 4TH ED., (1987), NATIONAL INSTITUTE OF HEALTH,BETHESDA,MD.). ENTRY 1- 9 10-26 27 28 29 KABAT 1- 9 11-27 27A 27B 27C ENTRY 30-97 110 111-172 173-203 204-216 KABAT 28-95 106A 107-168 170-200 203-215 2. THE LIGHT CHAIN WAS SEQUENCED BY FETT AND DEUTSCH (1974) BIOCHEMISTRY, 13, 4102-4114. 3. THIS COMPLEX WAS PREPARED BY DIFFUSION OF THE PEPTIDE INTO A CRYSTAL OF THE DIMER. THE 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
ReflectionResolution: 2.7→15 Å / Num. obs: 6067

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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
Rwork0.177 -
obs0.177 6067
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 0 0 3242
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.025
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.03
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_restr0.1150.15
X-RAY DIFFRACTIONp_singtor_nbd0.1860.5
X-RAY DIFFRACTIONp_multtor_nbd0.2610.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1830.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor7.97.9
X-RAY DIFFRACTIONp_staggered_tor25.125.1
X-RAY DIFFRACTIONp_orthonormal_tor24.824.8
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 6067 / σ(F): 1.5 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

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