data_1S4J # _entry.id 1S4J # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1S4J pdb_00001s4j 10.2210/pdb1s4j/pdb RCSB RCSB021357 ? ? WWPDB D_1000021357 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1S4H _pdbx_database_related.details 'C-terminus peptide of ribosamal P2 protein from L. brasiliensis' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1S4J _pdbx_database_status.recvd_initial_deposition_date 2004-01-16 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Soares, M.R.' 1 'Bisch, P.M.' 2 'Campos de Carvalho, A.C.' 3 'Valente, A.P.' 4 'Almeida, F.C.L.' 5 # _citation.id primary _citation.title ;Correlation between conformation and antibody binding: NMR structure of cross-reactive peptides from T. cruzi, human and L. braziliensis ; _citation.journal_abbrev 'Febs Lett.' _citation.journal_volume 560 _citation.page_first 134 _citation.page_last 140 _citation.year 2004 _citation.journal_id_ASTM FEBLAL _citation.country NE _citation.journal_id_ISSN 0014-5793 _citation.journal_id_CSD 0165 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 14988012 _citation.pdbx_database_id_DOI '10.1016/S0014-5793(04)00088-2' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Soares, M.R.' 1 ? primary 'Bisch, P.M.' 2 ? primary 'Campos De Carvalho, A.C.' 3 ? primary 'Valente, A.P.' 4 ? primary 'Almeida, F.C.L.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description '60S acidic ribosomal protein P2' _entity.formula_weight 1476.477 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'h13 - C-terminal domain' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Ribosomal P2 protein' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code EESDDDMGFGLFD _entity_poly.pdbx_seq_one_letter_code_can EESDDDMGFGLFD _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLU n 1 2 GLU n 1 3 SER n 1 4 ASP n 1 5 ASP n 1 6 ASP n 1 7 MET n 1 8 GLY n 1 9 PHE n 1 10 GLY n 1 11 LEU n 1 12 PHE n 1 13 ASP n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'peptide obtained by solid phase synthesis. the sequence is naturally found in Homo sapiens' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code RLA2_HUMAN _struct_ref.pdbx_db_accession P05387 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code EESDDDMGFGLFD _struct_ref.pdbx_align_begin 103 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1S4J _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 13 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P05387 _struct_ref_seq.db_align_beg 103 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 115 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 13 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 '2D TOCSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 278 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 5.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength '10mM phosphate buffer' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '2mM of peptide; 10% D2O; 10mM phosphate buffer at pH 5.5' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Bruker DRX 600 2 ? Bruker DRX 400 # _pdbx_nmr_refine.entry_id 1S4J _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1S4J _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear techniques.' # _pdbx_nmr_ensemble.entry_id 1S4J _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1S4J _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal NMRPipe 2.1 processing Delaglio 1 NMRView 5.03 'data analysis' 'Bruce A. Johnson' 2 CNS 1.1 'structure solution' Brunger 3 CNS 1.1 refinement Brunger 4 # _exptl.entry_id 1S4J _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1S4J _struct.title 'NMR structure of cross-reactive peptides from Homo sapiens' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1S4J _struct_keywords.pdbx_keywords RIBOSOME _struct_keywords.text 'antigenic peptide, ribosomal p2 protein, Chagas disease, RIBOSOME' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # _database_PDB_matrix.entry_id 1S4J _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1S4J _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLU 1 1 1 GLU GLU A . n A 1 2 GLU 2 2 2 GLU GLU A . n A 1 3 SER 3 3 3 SER SER A . n A 1 4 ASP 4 4 4 ASP ASP A . n A 1 5 ASP 5 5 5 ASP ASP A . n A 1 6 ASP 6 6 6 ASP ASP A . n A 1 7 MET 7 7 7 MET MET A . n A 1 8 GLY 8 8 8 GLY GLY A . n A 1 9 PHE 9 9 9 PHE PHE A . n A 1 10 GLY 10 10 10 GLY GLY A . n A 1 11 LEU 11 11 11 LEU LEU A . n A 1 12 PHE 12 12 12 PHE PHE A . n A 1 13 ASP 13 13 13 ASP ASP A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2004-03-16 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLU A 2 ? ? -126.01 -68.13 2 1 SER A 3 ? ? 55.53 10.82 3 1 ASP A 5 ? ? -129.10 -69.03 4 1 ASP A 6 ? ? -146.19 -48.27 5 2 GLU A 2 ? ? -95.80 -70.05 6 2 SER A 3 ? ? 53.47 8.44 7 2 ASP A 5 ? ? -129.82 -64.27 8 2 ASP A 6 ? ? -144.04 -56.87 9 2 PHE A 9 ? ? -90.05 -92.35 10 3 GLU A 2 ? ? -94.27 -71.12 11 3 SER A 3 ? ? 53.05 8.31 12 3 ASP A 5 ? ? -129.56 -64.57 13 3 ASP A 6 ? ? -146.40 -53.88 14 3 PHE A 9 ? ? -89.95 -81.36 15 4 SER A 3 ? ? 57.51 17.20 16 4 ASP A 5 ? ? -126.02 -62.12 17 4 ASP A 6 ? ? -153.24 -50.80 18 4 PHE A 9 ? ? -83.46 -78.74 19 5 GLU A 2 ? ? -95.18 -68.74 20 5 SER A 3 ? ? 53.31 8.69 21 5 ASP A 5 ? ? -129.75 -64.01 22 5 ASP A 6 ? ? -143.95 -57.42 23 5 PHE A 9 ? ? -89.54 -92.45 24 6 SER A 3 ? ? 54.00 9.70 25 6 ASP A 5 ? ? -129.11 -63.41 26 6 ASP A 6 ? ? -144.31 -58.21 27 6 PHE A 9 ? ? -89.40 -97.69 28 7 SER A 3 ? ? 53.81 9.36 29 7 ASP A 5 ? ? -129.21 -62.92 30 7 ASP A 6 ? ? -144.52 -58.49 31 7 PHE A 9 ? ? -90.37 -93.23 32 8 GLU A 2 ? ? -95.92 -68.00 33 8 SER A 3 ? ? 53.76 8.97 34 8 ASP A 5 ? ? -129.21 -63.84 35 8 ASP A 6 ? ? -143.96 -57.79 36 8 PHE A 9 ? ? -89.32 -96.83 37 9 GLU A 2 ? ? -126.92 -71.06 38 9 SER A 3 ? ? 55.05 9.25 39 9 ASP A 5 ? ? -130.15 -70.72 40 9 ASP A 6 ? ? -146.81 -44.69 41 9 PHE A 9 ? ? -90.98 -159.56 42 9 LEU A 11 ? ? 74.92 -18.97 43 10 GLU A 2 ? ? -106.87 -72.11 44 10 SER A 3 ? ? 54.77 12.15 45 10 ASP A 5 ? ? -126.31 -64.17 46 10 ASP A 6 ? ? -148.91 -53.71 47 10 MET A 7 ? ? -138.02 -157.74 48 10 PHE A 9 ? ? -91.92 -159.12 49 11 GLU A 2 ? ? -116.45 -75.56 50 11 SER A 3 ? ? 52.59 9.31 51 11 ASP A 5 ? ? -128.49 -64.27 52 11 ASP A 6 ? ? -145.22 -61.84 53 11 PHE A 9 ? ? -94.00 -87.78 54 12 GLU A 2 ? ? -127.19 -73.16 55 12 SER A 3 ? ? 56.47 1.81 56 12 ASP A 5 ? ? -139.85 -73.85 57 12 MET A 7 ? ? 63.87 -170.08 58 13 SER A 3 ? ? 55.36 167.47 59 13 ASP A 4 ? ? 44.28 13.08 60 13 ASP A 5 ? ? -100.75 -77.24 61 14 GLU A 2 ? ? -130.12 -70.35 62 14 SER A 3 ? ? 54.56 10.05 63 14 ASP A 5 ? ? -130.58 -66.87 64 14 ASP A 6 ? ? -147.97 -59.60 65 14 PHE A 9 ? ? -92.52 -159.21 66 14 LEU A 11 ? ? 74.82 -19.08 67 15 SER A 3 ? ? 53.81 9.51 68 15 ASP A 5 ? ? -129.36 -63.40 69 15 ASP A 6 ? ? -144.62 -57.87 70 15 PHE A 9 ? ? -89.89 -93.27 71 16 GLU A 2 ? ? -93.69 -72.27 72 16 SER A 3 ? ? 53.32 8.71 73 16 ASP A 5 ? ? -129.32 -65.06 74 16 ASP A 6 ? ? -147.09 -55.88 75 16 PHE A 9 ? ? -89.60 -75.43 76 17 GLU A 2 ? ? -95.87 -70.10 77 17 SER A 3 ? ? 53.74 8.87 78 17 ASP A 5 ? ? -129.32 -64.32 79 17 ASP A 6 ? ? -143.67 -57.96 80 17 PHE A 9 ? ? -89.21 -94.71 81 18 GLU A 2 ? ? -98.07 -65.78 82 18 SER A 3 ? ? 55.43 1.69 83 18 ASP A 5 ? ? -138.00 -71.27 84 18 ASP A 6 ? ? -156.40 86.66 85 18 MET A 7 ? ? 63.99 -171.40 86 18 PHE A 9 ? ? -88.36 -102.78 87 19 GLU A 2 ? ? -98.48 -67.44 88 19 SER A 3 ? ? 55.61 2.81 89 19 ASP A 5 ? ? -138.46 -72.86 90 19 ASP A 6 ? ? -154.98 84.88 91 19 MET A 7 ? ? 64.25 -166.66 92 19 PHE A 9 ? ? -88.23 -107.69 93 20 SER A 3 ? ? 54.45 11.56 94 20 ASP A 5 ? ? -128.00 -62.62 95 20 ASP A 6 ? ? -146.47 -57.28 96 20 PHE A 9 ? ? -92.90 -101.30 97 20 LEU A 11 ? ? 75.16 -63.98 98 20 PHE A 12 ? ? 31.42 -80.56 #