data_2KNS # _entry.id 2KNS # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2KNS pdb_00002kns 10.2210/pdb2kns/pdb RCSB RCSB101350 ? ? WWPDB D_1000101350 ? ? # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KNS _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2009-09-03 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.pdb_format_compatible Y _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 'Bhunia, A.' 1 'Bhattacharjya, S.' 2 'Ramamoorthy, A.' 3 # _citation.id primary _citation.title ;NMR structure of pardaxin, a pore-forming antimicrobial peptide, in lipopolysaccharide Micelles: Mechanism of outer membrane permeabilization ; _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 285 _citation.page_first 3883 _citation.page_last 3895 _citation.year 2010 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19959835 _citation.pdbx_database_id_DOI 10.1074/jbc.M109.065672 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bhunia, A.' 1 ? primary 'Domadia, P.N.' 2 ? primary 'Torres, J.' 3 ? primary 'Hallock, K.J.' 4 ? primary 'Ramamoorthy, A.' 5 ? primary 'Bhattacharjya, S.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Pardaxin P-4' _entity.formula_weight 3325.851 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Pardaxin Pa4, Pardaxin P1a' # _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 GFFALIPKIISSPLFKTLLSAVGSALSSSGGQE _entity_poly.pdbx_seq_one_letter_code_can GFFALIPKIISSPLFKTLLSAVGSALSSSGGQE _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 GLY n 1 2 PHE n 1 3 PHE n 1 4 ALA n 1 5 LEU n 1 6 ILE n 1 7 PRO n 1 8 LYS n 1 9 ILE n 1 10 ILE n 1 11 SER n 1 12 SER n 1 13 PRO n 1 14 LEU n 1 15 PHE n 1 16 LYS n 1 17 THR n 1 18 LEU n 1 19 LEU n 1 20 SER n 1 21 ALA n 1 22 VAL n 1 23 GLY n 1 24 SER n 1 25 ALA n 1 26 LEU n 1 27 SER n 1 28 SER n 1 29 SER n 1 30 GLY n 1 31 GLY n 1 32 GLN n 1 33 GLU 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 'Pardachirus marmoratus' _pdbx_entity_src_syn.organism_common_name 'Red sea moses sole' _pdbx_entity_src_syn.ncbi_taxonomy_id 31087 _pdbx_entity_src_syn.details 'Standard F-moc solid phase peptide synthesis' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PAP4_PARMA _struct_ref.pdbx_db_accession P81861 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GFFALIPKIISSPLFKTLLSAVGSALSSSGGQE _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2KNS _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 33 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P81861 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 33 _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 33 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H trNOESY' 1 2 1 '2D 1H-1H TOCSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH 4.5 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 288 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '0.5mM Pardaxin-1; 90% H2O/10% D2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DRX _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker DRX' # _pdbx_nmr_refine.entry_id 2KNS _pdbx_nmr_refine.method 'distance geometry' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2KNS _pdbx_nmr_details.text 'The structure was determined based on NOE' # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'target function' _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KNS _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.representative_conformer 1 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2KNS _pdbx_nmr_representative.selection_criteria 'lowest energy' # _pdbx_nmr_software.authors 'Guntert, Braun and Wuthrich' _pdbx_nmr_software.classification refinement _pdbx_nmr_software.name DYANA _pdbx_nmr_software.version 1.5 _pdbx_nmr_software.ordinal 1 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2KNS _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KNS _struct.title 'Helical Hairpin Structure of Pardaxin in Lipopolysaccharide Micelles: Studied by NMR Spectroscopy' _struct.pdbx_model_details 'lowest energy, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KNS _struct_keywords.pdbx_keywords 'ANTIMICROBIAL PROTEIN' _struct_keywords.text ;Pardaxin, Pa4, LPS, trNOE, antimicrobial peptide, STD NMR, Ion transport, Porin, Secreted, Toxin, Transmembrane, Transport, ANTIMICROBIAL PROTEIN ; # _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.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ALA A 4 ? SER A 12 ? ALA A 4 SER A 12 1 ? 9 HELX_P HELX_P2 2 PHE A 15 ? SER A 27 ? PHE A 15 SER A 27 1 ? 13 HELX_P HELX_P3 3 SER A 29 ? GLU A 33 ? SER A 29 GLU A 33 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 2KNS _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 # 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 GLY 1 1 1 GLY GLY A . n A 1 2 PHE 2 2 2 PHE PHE A . n A 1 3 PHE 3 3 3 PHE PHE A . n A 1 4 ALA 4 4 4 ALA ALA A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 ILE 6 6 6 ILE ILE A . n A 1 7 PRO 7 7 7 PRO PRO A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 ILE 9 9 9 ILE ILE A . n A 1 10 ILE 10 10 10 ILE ILE A . n A 1 11 SER 11 11 11 SER SER A . n A 1 12 SER 12 12 12 SER SER A . n A 1 13 PRO 13 13 13 PRO PRO A . n A 1 14 LEU 14 14 14 LEU LEU A . n A 1 15 PHE 15 15 15 PHE PHE A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 THR 17 17 17 THR THR A . n A 1 18 LEU 18 18 18 LEU LEU A . n A 1 19 LEU 19 19 19 LEU LEU A . n A 1 20 SER 20 20 20 SER SER A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 VAL 22 22 22 VAL VAL A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 SER 24 24 24 SER SER A . n A 1 25 ALA 25 25 25 ALA ALA A . n A 1 26 LEU 26 26 26 LEU LEU A . n A 1 27 SER 27 27 27 SER SER A . n A 1 28 SER 28 28 28 SER SER A . n A 1 29 SER 29 29 29 SER SER A . n A 1 30 GLY 30 30 30 GLY GLY A . n A 1 31 GLY 31 31 31 GLY GLY A . n A 1 32 GLN 32 32 32 GLN GLN A . n A 1 33 GLU 33 33 33 GLU GLU 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 2009-12-15 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 # _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' 'Database references' 3 3 '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 3 'Structure model' database_2 2 3 'Structure model' pdbx_struct_assembly 3 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_nmr_exptl_sample.component Pardaxin-1 _pdbx_nmr_exptl_sample.concentration 0.5 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling ? _pdbx_nmr_exptl_sample.solution_id 1 # 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 SER A 12 ? ? -88.57 -71.27 2 1 PRO A 13 ? ? -69.72 -173.47 3 2 SER A 12 ? ? -91.70 -73.79 4 2 PRO A 13 ? ? -69.73 -176.17 5 3 SER A 12 ? ? -88.86 -71.62 6 3 PRO A 13 ? ? -69.71 -174.15 7 4 SER A 12 ? ? -88.67 -71.24 8 4 PRO A 13 ? ? -69.81 -173.23 9 5 SER A 12 ? ? -92.41 -72.98 10 5 PRO A 13 ? ? -69.72 -174.98 11 6 SER A 12 ? ? -92.54 -73.23 12 6 PRO A 13 ? ? -69.68 -174.85 13 7 SER A 12 ? ? -91.26 -72.12 14 7 PRO A 13 ? ? -69.82 -173.66 15 8 SER A 12 ? ? -90.64 -72.73 16 8 PRO A 13 ? ? -69.79 -174.79 17 9 SER A 12 ? ? -91.97 -73.33 18 9 PRO A 13 ? ? -69.79 -175.68 19 10 SER A 12 ? ? -88.57 -71.12 20 10 PRO A 13 ? ? -69.75 -173.38 21 11 SER A 12 ? ? -90.61 -72.76 22 11 PRO A 13 ? ? -69.77 -174.84 23 12 SER A 12 ? ? -91.27 -73.28 24 12 PRO A 13 ? ? -69.76 -175.37 25 13 SER A 12 ? ? -90.79 -72.99 26 13 PRO A 13 ? ? -69.77 -175.15 27 14 PRO A 13 ? ? -69.71 -173.00 28 15 SER A 12 ? ? -90.70 -72.74 29 15 PRO A 13 ? ? -69.83 -174.82 30 16 SER A 12 ? ? -88.63 -71.20 31 16 PRO A 13 ? ? -69.81 -173.36 32 17 SER A 12 ? ? -90.96 -72.65 33 17 PRO A 13 ? ? -69.75 -173.82 34 18 SER A 12 ? ? -90.70 -72.80 35 18 PRO A 13 ? ? -69.70 -174.80 36 19 SER A 12 ? ? -88.45 -70.93 37 19 PRO A 13 ? ? -69.84 -174.03 38 20 PRO A 13 ? ? -69.72 -172.63 #