data_1SKL # _entry.id 1SKL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1SKL RCSB RCSB021792 WWPDB D_1000021792 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1SKI . unspecified PDB 1SKK . unspecified # _pdbx_database_status.entry_id 1SKL _pdbx_database_status.status_code REL _pdbx_database_status.recvd_initial_deposition_date 2004-03-05 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry N _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Appelt, C.' 1 'Soderhall, J.A.' 2 'Bienert, M.' 3 'Dathe, M.' 4 'Schmieder, P.' 5 # _citation.id primary _citation.title 'Structure of the antimicrobial, cationic hexapeptide cyclo(RRWWRF) and its analogues in solution and bound to detergent micelles.' _citation.journal_abbrev Chembiochem _citation.journal_volume 6 _citation.page_first 1654 _citation.page_last 1662 _citation.year 2005 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1439-4227 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16075425 _citation.pdbx_database_id_DOI 10.1002/cbic.200500095 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Appelt, C.' 1 primary 'Wessolowski, A.' 2 primary 'Soderhall, J.A.' 3 primary 'Dathe, M.' 4 primary 'Schmieder, P.' 5 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'cyclic hexapeptide RR(NAL)(NAL)RF' _entity.formula_weight 1031.236 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details 'NAL = L-2-Naphtylalanine' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'RR(NAL)(NAL)RF' _entity_poly.pdbx_seq_one_letter_code_can RRAARF _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 ARG n 1 2 ARG n 1 3 NAL n 1 4 NAL n 1 5 ARG n 1 6 PHE 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 ;Synthesis of the linear peptide by the solid-phase method using standard Fmoc chemistry in continuous flow mode (MilliGen 9050 peptide synthesizer; Millipore, USA). Cyclization manually by applying HAPyU-chemistry. Purification by RP-HPLC (Shimadzu LC-10AD system), Characterization by matrix-assisted laser desorption mass spectrometry (MALDI II, Kratos, Manchester, UK). ; # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 1SKL _struct_ref.pdbx_db_accession 1SKL _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code 'RR(NAL)(NAL)RF' _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1SKL _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 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1SKL _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _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 6 # 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 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 NAL 'L-peptide linking' n 'BETA-(2-NAPHTHYL)-ALANINE' ? 'C13 H13 N O2' 215.248 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 # 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' 3 1 1 DQF-COSY # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 300 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 6.3 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _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 '2.5 mM c-RY, 50 mM D38 dodecyl phosphocholine' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DRX _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1SKL _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ;103 distance restraints, 2 dihedral restraints ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1SKL _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _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 1SKL _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal XWINNMR 2.6 collection Bruker 1 SPARKY 3.1 'data analysis' 'Goddard, T.D. and Kneller, D.G.' 2 AMBER 6 'structure solution' 'Case, D.A. et al' 3 AMBER 6 refinement 'Case, D.A. et al' 4 # _exptl.entry_id 1SKL _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1SKL _struct.title 'Structure of the antimicrobial hexapeptide cyc-(RRNalNalRF) bound to DPC micelles' _struct.pdbx_descriptor 'cyclic hexapeptide RR(NAL)(NAL)RF' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1SKL _struct_keywords.pdbx_keywords 'ANTIMICROBIAL PROTEIN' _struct_keywords.text 'cyclic peptide; antimicrobial peptide, 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_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A ARG 1 N ? ? ? 1_555 A PHE 6 C ? ? A ARG 1 A PHE 6 1_555 ? ? ? ? ? ? ? 1.347 ? covale2 covale ? ? A ARG 2 C ? ? ? 1_555 A NAL 3 N ? ? A ARG 2 A NAL 3 1_555 ? ? ? ? ? ? ? 1.345 ? covale3 covale ? ? A NAL 3 C ? ? ? 1_555 A NAL 4 N ? ? A NAL 3 A NAL 4 1_555 ? ? ? ? ? ? ? 1.346 ? covale4 covale ? ? A NAL 4 C ? ? ? 1_555 A ARG 5 N ? ? A NAL 4 A ARG 5 1_555 ? ? ? ? ? ? ? 1.348 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 1SKL _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 ARG 1 1 1 ARG ARG A . n A 1 2 ARG 2 2 2 ARG ARG A . n A 1 3 NAL 3 3 3 NAL NAL A . n A 1 4 NAL 4 4 4 NAL NAL A . n A 1 5 ARG 5 5 5 ARG ARG A . n A 1 6 PHE 6 6 6 PHE PHE A . n # _pdbx_molecule_features.prd_id PRD_000102 _pdbx_molecule_features.name 'CYCLIC HEXAPEPTIDE RR(NAL)(NAL)RF' _pdbx_molecule_features.type 'Cyclic peptide' _pdbx_molecule_features.class Antimicrobial _pdbx_molecule_features.details ? # _pdbx_molecule.instance_id 1 _pdbx_molecule.prd_id PRD_000102 _pdbx_molecule.asym_id A # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A NAL 3 A NAL 3 ? ALA 'BETA-(2-NAPHTHYL)-ALANINE' 2 A NAL 4 A NAL 4 ? ALA 'BETA-(2-NAPHTHYL)-ALANINE' # _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 2005-03-15 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-08-03 5 'Structure model' 1 4 2012-12-12 # _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 ? # 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' 'Non-polymer description' 4 5 'Structure model' Other # 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 NAL A 3 ? ? -173.80 -13.90 2 1 ARG A 5 ? ? 33.45 15.50 3 2 ARG A 2 ? ? -134.00 -64.88 4 2 NAL A 3 ? ? -175.05 -0.07 5 2 NAL A 4 ? ? -144.57 -62.59 6 2 ARG A 5 ? ? -144.19 -22.93 7 3 NAL A 3 ? ? -178.03 14.73 8 3 NAL A 4 ? ? -150.53 -153.38 9 4 NAL A 3 ? ? -169.23 -2.19 10 4 NAL A 4 ? ? -146.29 -57.90 11 4 ARG A 5 ? ? -149.19 -19.22 12 5 NAL A 3 ? ? -175.12 4.01 13 5 NAL A 4 ? ? -152.50 -151.64 14 6 NAL A 3 ? ? -174.12 3.05 15 6 NAL A 4 ? ? -149.70 -140.43 16 6 ARG A 5 ? ? -60.13 6.20 17 7 NAL A 3 ? ? -168.54 10.04 18 7 NAL A 4 ? ? -140.51 -57.68 19 7 ARG A 5 ? ? -167.86 -25.97 20 8 ARG A 2 ? ? -123.84 -65.61 21 8 NAL A 3 ? ? -168.53 5.91 22 8 NAL A 4 ? ? -146.52 -53.13 23 8 ARG A 5 ? ? -164.99 -28.36 24 9 NAL A 3 ? ? -177.34 4.83 25 9 NAL A 4 ? ? -147.44 -140.75 26 10 ARG A 2 ? ? -138.57 -57.14 27 10 NAL A 3 ? ? -170.62 9.68 28 10 NAL A 4 ? ? -147.20 -159.46 #