data_9EPS # _entry.id 9EPS # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.409 _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 9EPS pdb_00009eps 10.2210/pdb9eps/pdb WWPDB D_1292137386 ? ? BMRB 34911 ? 10.13018/BMR34911 # 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 _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2025-02-26 ? 2 'Structure model' 1 1 2026-01-14 ? # _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 ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # 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 2 'Structure model' citation 2 2 'Structure model' citation_author # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_CSD' 4 2 'Structure model' '_citation.journal_id_ISSN' 5 2 'Structure model' '_citation.page_first' 6 2 'Structure model' '_citation.page_last' 7 2 'Structure model' '_citation.pdbx_database_id_DOI' 8 2 'Structure model' '_citation.pdbx_database_id_PubMed' 9 2 'Structure model' '_citation.title' 10 2 'Structure model' '_citation.year' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr . _pdbx_database_status.entry_id 9EPS _pdbx_database_status.recvd_initial_deposition_date 2024-03-19 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs . _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'NMR structure of MDN-0066 in micellar DPC solution' _pdbx_database_related.db_id 34911 _pdbx_database_related.content_type unspecified # _pdbx_contact_author.id 2 _pdbx_contact_author.email jose.martins@ugent.be _pdbx_contact_author.name_first Jose _pdbx_contact_author.name_last Martins _pdbx_contact_author.name_mi C. _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-7350-2253 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kovacs, B.' 1 0000-0003-2715-5793 'Geudens, N.' 2 0000-0003-0459-7142 'Martins, J.C.' 3 0000-0001-7350-2253 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country DE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Adv Sci' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2198-3844 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first e20365 _citation.page_last e20365 _citation.title 'Higher-Level Structural Classification of Pseudomonas Cyclic Lipopeptides through Their Bioactive Conformation.' _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/advs.202520365 _citation.pdbx_database_id_PubMed 41391051 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kovacs, B.' 1 0000-0003-2715-5793 primary 'Prasad, D.' 2 0000-0002-0266-3401 primary 'De Roo, V.' 3 0000-0002-3418-3285 primary 'Vanheede, M.' 4 0000-0002-6189-2618 primary 'Muangkaew, P.' 5 ? primary 'Madder, A.' 6 0000-0003-0179-7608 primary 'Hofte, M.' 7 0000-0002-0850-3249 primary 'De Mot, R.' 8 0000-0002-0030-9441 primary 'Geudens, N.' 9 0000-0003-0459-7142 primary 'Martins, J.C.' 10 0000-0001-7350-2253 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer nat MDN-0066 901.100 1 ? ? ? ;1) The polypeptide chain of MDN-0066 consists of 8amino acids. 2) The N-terminal amino acid (DLE) is acylated with an (R)-3-hydroxy-decanoic acid (IG8) moeity which is indicated as the first residue. 3) The depsi (ester) bond is established between the ILE9 carboxyl and 2TL4 side-chain OH group. ; 2 non-polymer syn '(3~{R})-3-oxidanyldecanoic acid' 188.264 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(D)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DLE)(DGL)(2TL)L(DLE)(DSN)LI' _entity_poly.pdbx_seq_one_letter_code_can LETLLSLI _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name '(3~{R})-3-oxidanyldecanoic acid' _pdbx_entity_nonpoly.comp_id IG8 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DLE n 1 2 DGL n 1 3 2TL n 1 4 LEU n 1 5 DLE n 1 6 DSN n 1 7 LEU n 1 8 ILE n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num 1 _entity_src_nat.pdbx_end_seq_num 8 _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Pseudomonas azadiae' _entity_src_nat.pdbx_ncbi_taxonomy_id 2843612 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain SWRI103 _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # 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 2TL 'D-peptide linking' . D-allothreonine ? 'C4 H9 N O3' 119.119 DGL 'D-peptide linking' . 'D-GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 DLE 'D-peptide linking' . D-LEUCINE ? 'C6 H13 N O2' 131.173 DSN 'D-peptide linking' . D-SERINE ? 'C3 H7 N O3' 105.093 IG8 non-polymer . '(3~{R})-3-oxidanyldecanoic acid' ? 'C10 H20 O3' 188.264 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 # 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 DLE 1 2 2 DLE DLE A . n A 1 2 DGL 2 3 3 DGL DGL A . n A 1 3 2TL 3 4 4 2TL 2TL A . n A 1 4 LEU 4 5 5 LEU LEU A . n A 1 5 DLE 5 6 6 DLE DLE A . n A 1 6 DSN 6 7 7 DSN DSN A . n A 1 7 LEU 7 8 8 LEU LEU A . n A 1 8 ILE 8 9 9 ILE ILE A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id IG8 _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id IG8 _pdbx_nonpoly_scheme.auth_mon_id IG8 _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9EPS _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 9EPS _struct.title 'NMR structure of MDN-0066 in micellar DPC solution' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9EPS _struct_keywords.text 'Non-ribosomal polypeptide, Cyclic lipodepsipeptide, Antimicrobial peptide, Biosurfactant, SURFACTANT PROTEIN' _struct_keywords.pdbx_keywords 'SURFACTANT PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9EPS _struct_ref.pdbx_db_accession 9EPS _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 9EPS _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 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 9EPS _struct_ref_seq.db_align_beg 2 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 9 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 9 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_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,B # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'NMR Distance Restraints' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _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] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id 2TL _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 3 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id LEU _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 7 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id 2TL _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 4 _struct_conf.end_auth_comp_id LEU _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 8 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 _struct_conn.pdbx_role covale1 covale both ? A DLE 1 C ? ? ? 1_555 A DGL 2 N ? ? A DLE 2 A DGL 3 1_555 ? ? ? ? ? ? ? 1.314 ? ? covale2 covale both ? A DLE 1 N ? ? ? 1_555 B IG8 . C ? ? A DLE 2 A IG8 101 1_555 ? ? ? ? ? ? ? 1.307 ? ? covale3 covale both ? A DGL 2 C ? ? ? 1_555 A 2TL 3 N ? ? A DGL 3 A 2TL 4 1_555 ? ? ? ? ? ? ? 1.320 ? ? covale4 covale both ? A 2TL 3 C ? ? ? 1_555 A LEU 4 N ? ? A 2TL 4 A LEU 5 1_555 ? ? ? ? ? ? ? 1.351 ? ? covale5 covale one ? A 2TL 3 OG1 ? ? ? 1_555 A ILE 8 C ? ? A 2TL 4 A ILE 9 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale6 covale both ? A LEU 4 C ? ? ? 1_555 A DLE 5 N ? ? A LEU 5 A DLE 6 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale7 covale both ? A DLE 5 C ? ? ? 1_555 A DSN 6 N ? ? A DLE 6 A DSN 7 1_555 ? ? ? ? ? ? ? 1.350 ? ? covale8 covale both ? A DSN 6 C ? ? ? 1_555 A LEU 7 N ? ? A DSN 7 A LEU 8 1_555 ? ? ? ? ? ? ? 1.411 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_modification_feature.ordinal _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.label_alt_id _pdbx_modification_feature.modified_residue_label_comp_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_modification_feature.modified_residue_label_alt_id _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.PDB_ins_code _pdbx_modification_feature.symmetry _pdbx_modification_feature.modified_residue_auth_comp_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_PDB_ins_code _pdbx_modification_feature.modified_residue_symmetry _pdbx_modification_feature.comp_id_linking_atom _pdbx_modification_feature.modified_residue_id_linking_atom _pdbx_modification_feature.modified_residue_id _pdbx_modification_feature.ref_pcm_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.type _pdbx_modification_feature.category 1 2TL A 3 ? . . . . 2TL A 4 ? 1_555 . . . . . . . DTH 1 2TL Stereoisomerisation 'Named protein modification' 2 IG8 B . ? DLE A 1 ? IG8 A 101 ? 1_555 DLE A 2 ? 1_555 C N DLE 2 IG8 None Lipid/lipid-like 3 2TL A 3 ? ILE A 8 ? 2TL A 4 ? 1_555 ILE A 9 ? 1_555 OG1 C . . . None 'Non-standard linkage' # _pdbx_entry_details.entry_id 9EPS _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_protein_modification Y # 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 DSN A 7 ? ? 144.40 -22.22 2 2 LEU A 5 ? ? 43.53 75.63 3 3 LEU A 5 ? ? 43.63 75.43 4 4 LEU A 5 ? ? 47.09 76.53 5 5 LEU A 5 ? ? 46.25 79.29 6 6 LEU A 5 ? ? 46.53 79.65 7 7 LEU A 5 ? ? 43.66 75.36 8 8 LEU A 5 ? ? 43.38 74.66 9 9 LEU A 5 ? ? 43.59 76.31 10 10 LEU A 5 ? ? 43.69 75.75 11 11 LEU A 5 ? ? 46.40 79.74 # _pdbx_validate_main_chain_plane.id 1 _pdbx_validate_main_chain_plane.PDB_model_num 1 _pdbx_validate_main_chain_plane.auth_comp_id LEU _pdbx_validate_main_chain_plane.auth_asym_id A _pdbx_validate_main_chain_plane.auth_seq_id 5 _pdbx_validate_main_chain_plane.PDB_ins_code ? _pdbx_validate_main_chain_plane.label_alt_id ? _pdbx_validate_main_chain_plane.improper_torsion_angle 12.02 # _pdbx_nmr_ensemble.entry_id 9EPS _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 11 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _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 9EPS _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '1.5 mM MDN-0066, 104.3 mM [U-2H] DPC, 90% H2O/10% D2O' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' _pdbx_nmr_sample_details.label 1H _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details ;MDN-0066 was dissolved in the micellar solution of uniformly deuterated dodecylphosphocholine (DPC-d38). Solvent: 10 mM Na2HPO4/NaH2PO4 buffer at pH 7.4. ; # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 MDN-0066 1.5 ? mM 'natural abundance' 1 DPC 104.3 ? mM '[U-2H]' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7.4 _pdbx_nmr_exptl_sample_conditions.ionic_strength '26 (buffer only)' _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label conditions_1 _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '2D 1H-1H NOESY' 1 isotropic 2 1 1 '2D 1H-1H TOCSY' 1 isotropic 3 1 1 '2D 1H-1H COSY' 1 isotropic 4 1 1 '2D 1H-13C HSQC' 1 isotropic # _pdbx_nmr_refine.entry_id 9EPS _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ;The lowest energy NMR structure issued from CNS was refined using unrestrained AMBER molecular dynamics simulations (against the ff14SB force field). Here, we modelled the interaction of a single peptide molecule with an explicit dodecylphosphocholine (DPC) micelle. The representative peptide conformation of the trajectory (=refined structure) was selected using cluster analysis. Solvent model: TIP3P. Occasional too-close contacts present in the NMR structure ensemble (structures #2-#11) are fully removed during the AMBER moleculary dynamics refinement (structure #1) ; _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 refinement Amber ? 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' 2 'data analysis' AmberTools ? 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' 3 processing TopSpin 3.x 'Bruker Biospin' 4 collection TopSpin 3.x 'Bruker Biospin' 5 'peak picking' 'CcpNmr Analysis' ? 'Vuister et al.' 6 'structure calculation' CNS ? 'Brunger, Adams, Clore, Gros, Nilges and Read' 7 'chemical shift assignment' 'CcpNmr Analysis' ? 'Vuister et al.' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 2TL N N N N 1 2TL CA C N R 2 2TL CB C N R 3 2TL OG1 O N N 4 2TL CG2 C N N 5 2TL C C N N 6 2TL O O N N 7 2TL OXT O N N 8 2TL H H N N 9 2TL H2 H N N 10 2TL HA H N N 11 2TL HB H N N 12 2TL HG1 H N N 13 2TL HG21 H N N 14 2TL HG22 H N N 15 2TL HG23 H N N 16 2TL HXT H N N 17 DGL N N N N 18 DGL CA C N R 19 DGL C C N N 20 DGL O O N N 21 DGL CB C N N 22 DGL CG C N N 23 DGL CD C N N 24 DGL OE1 O N N 25 DGL OE2 O N N 26 DGL OXT O N N 27 DGL H H N N 28 DGL H2 H N N 29 DGL HA H N N 30 DGL HB2 H N N 31 DGL HB3 H N N 32 DGL HG2 H N N 33 DGL HG3 H N N 34 DGL HE2 H N N 35 DGL HXT H N N 36 DLE N N N N 37 DLE CA C N R 38 DLE CB C N N 39 DLE CG C N N 40 DLE CD1 C N N 41 DLE CD2 C N N 42 DLE C C N N 43 DLE O O N N 44 DLE OXT O N N 45 DLE H H N N 46 DLE H2 H N N 47 DLE HA H N N 48 DLE HB2 H N N 49 DLE HB3 H N N 50 DLE HG H N N 51 DLE HD11 H N N 52 DLE HD12 H N N 53 DLE HD13 H N N 54 DLE HD21 H N N 55 DLE HD22 H N N 56 DLE HD23 H N N 57 DLE HXT H N N 58 DSN N N N N 59 DSN CA C N R 60 DSN C C N N 61 DSN O O N N 62 DSN OXT O N N 63 DSN CB C N N 64 DSN OG O N N 65 DSN H H N N 66 DSN H2 H N N 67 DSN HA H N N 68 DSN HXT H N N 69 DSN HB2 H N N 70 DSN HB3 H N N 71 DSN HG H N N 72 IG8 CA C N N 73 IG8 C C N N 74 IG8 O O N N 75 IG8 CB C N R 76 IG8 CG2 C N N 77 IG8 OG1 O N N 78 IG8 CD C N N 79 IG8 CE C N N 80 IG8 CZ C N N 81 IG8 CH C N N 82 IG8 CI C N N 83 IG8 CT C N N 84 IG8 O1 O N N 85 IG8 HA1 H N N 86 IG8 HA2 H N N 87 IG8 HB H N N 88 IG8 HG21 H N N 89 IG8 HG22 H N N 90 IG8 HG1 H N N 91 IG8 HD1 H N N 92 IG8 HD2 H N N 93 IG8 HE1 H N N 94 IG8 HE2 H N N 95 IG8 HZ1 H N N 96 IG8 HZ2 H N N 97 IG8 HH1 H N N 98 IG8 HH2 H N N 99 IG8 HI2 H N N 100 IG8 HI3 H N N 101 IG8 HI1 H N N 102 IG8 HT1 H N N 103 IG8 HT2 H N N 104 IG8 H1 H N N 105 ILE N N N N 106 ILE CA C N S 107 ILE C C N N 108 ILE O O N N 109 ILE CB C N S 110 ILE CG1 C N N 111 ILE CG2 C N N 112 ILE CD1 C N N 113 ILE OXT O N N 114 ILE H H N N 115 ILE H2 H N N 116 ILE HA H N N 117 ILE HB H N N 118 ILE HG12 H N N 119 ILE HG13 H N N 120 ILE HG21 H N N 121 ILE HG22 H N N 122 ILE HG23 H N N 123 ILE HD11 H N N 124 ILE HD12 H N N 125 ILE HD13 H N N 126 ILE HXT H N N 127 LEU N N N N 128 LEU CA C N S 129 LEU C C N N 130 LEU O O N N 131 LEU CB C N N 132 LEU CG C N N 133 LEU CD1 C N N 134 LEU CD2 C N N 135 LEU OXT O N N 136 LEU H H N N 137 LEU H2 H N N 138 LEU HA H N N 139 LEU HB2 H N N 140 LEU HB3 H N N 141 LEU HG H N N 142 LEU HD11 H N N 143 LEU HD12 H N N 144 LEU HD13 H N N 145 LEU HD21 H N N 146 LEU HD22 H N N 147 LEU HD23 H N N 148 LEU HXT H N N 149 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 2TL N CA sing N N 1 2TL CA CB sing N N 2 2TL CA C sing N N 3 2TL CB OG1 sing N N 4 2TL CB CG2 sing N N 5 2TL C O doub N N 6 2TL C OXT sing N N 7 2TL N H sing N N 8 2TL N H2 sing N N 9 2TL CA HA sing N N 10 2TL CB HB sing N N 11 2TL OG1 HG1 sing N N 12 2TL CG2 HG21 sing N N 13 2TL CG2 HG22 sing N N 14 2TL CG2 HG23 sing N N 15 2TL OXT HXT sing N N 16 DGL N CA sing N N 17 DGL N H sing N N 18 DGL N H2 sing N N 19 DGL CA C sing N N 20 DGL CA CB sing N N 21 DGL CA HA sing N N 22 DGL C O doub N N 23 DGL C OXT sing N N 24 DGL CB CG sing N N 25 DGL CB HB2 sing N N 26 DGL CB HB3 sing N N 27 DGL CG CD sing N N 28 DGL CG HG2 sing N N 29 DGL CG HG3 sing N N 30 DGL CD OE1 doub N N 31 DGL CD OE2 sing N N 32 DGL OE2 HE2 sing N N 33 DGL OXT HXT sing N N 34 DLE N CA sing N N 35 DLE N H sing N N 36 DLE N H2 sing N N 37 DLE CA CB sing N N 38 DLE CA C sing N N 39 DLE CA HA sing N N 40 DLE CB CG sing N N 41 DLE CB HB2 sing N N 42 DLE CB HB3 sing N N 43 DLE CG CD1 sing N N 44 DLE CG CD2 sing N N 45 DLE CG HG sing N N 46 DLE CD1 HD11 sing N N 47 DLE CD1 HD12 sing N N 48 DLE CD1 HD13 sing N N 49 DLE CD2 HD21 sing N N 50 DLE CD2 HD22 sing N N 51 DLE CD2 HD23 sing N N 52 DLE C O doub N N 53 DLE C OXT sing N N 54 DLE OXT HXT sing N N 55 DSN N CA sing N N 56 DSN N H sing N N 57 DSN N H2 sing N N 58 DSN CA C sing N N 59 DSN CA CB sing N N 60 DSN CA HA sing N N 61 DSN C O doub N N 62 DSN C OXT sing N N 63 DSN OXT HXT sing N N 64 DSN CB OG sing N N 65 DSN CB HB2 sing N N 66 DSN CB HB3 sing N N 67 DSN OG HG sing N N 68 IG8 OG1 CB sing N N 69 IG8 C CA sing N N 70 IG8 C O doub N N 71 IG8 CA CB sing N N 72 IG8 CB CG2 sing N N 73 IG8 CG2 CD sing N N 74 IG8 CD CE sing N N 75 IG8 CE CZ sing N N 76 IG8 CZ CH sing N N 77 IG8 CH CT sing N N 78 IG8 CT CI sing N N 79 IG8 C O1 sing N N 80 IG8 CA HA1 sing N N 81 IG8 CA HA2 sing N N 82 IG8 CB HB sing N N 83 IG8 CG2 HG21 sing N N 84 IG8 CG2 HG22 sing N N 85 IG8 OG1 HG1 sing N N 86 IG8 CD HD1 sing N N 87 IG8 CD HD2 sing N N 88 IG8 CE HE1 sing N N 89 IG8 CE HE2 sing N N 90 IG8 CZ HZ1 sing N N 91 IG8 CZ HZ2 sing N N 92 IG8 CH HH1 sing N N 93 IG8 CH HH2 sing N N 94 IG8 CI HI2 sing N N 95 IG8 CI HI3 sing N N 96 IG8 CI HI1 sing N N 97 IG8 CT HT1 sing N N 98 IG8 CT HT2 sing N N 99 IG8 O1 H1 sing N N 100 ILE N CA sing N N 101 ILE N H sing N N 102 ILE N H2 sing N N 103 ILE CA C sing N N 104 ILE CA CB sing N N 105 ILE CA HA sing N N 106 ILE C O doub N N 107 ILE C OXT sing N N 108 ILE CB CG1 sing N N 109 ILE CB CG2 sing N N 110 ILE CB HB sing N N 111 ILE CG1 CD1 sing N N 112 ILE CG1 HG12 sing N N 113 ILE CG1 HG13 sing N N 114 ILE CG2 HG21 sing N N 115 ILE CG2 HG22 sing N N 116 ILE CG2 HG23 sing N N 117 ILE CD1 HD11 sing N N 118 ILE CD1 HD12 sing N N 119 ILE CD1 HD13 sing N N 120 ILE OXT HXT sing N N 121 LEU N CA sing N N 122 LEU N H sing N N 123 LEU N H2 sing N N 124 LEU CA C sing N N 125 LEU CA CB sing N N 126 LEU CA HA sing N N 127 LEU C O doub N N 128 LEU C OXT sing N N 129 LEU CB CG sing N N 130 LEU CB HB2 sing N N 131 LEU CB HB3 sing N N 132 LEU CG CD1 sing N N 133 LEU CG CD2 sing N N 134 LEU CG HG sing N N 135 LEU CD1 HD11 sing N N 136 LEU CD1 HD12 sing N N 137 LEU CD1 HD13 sing N N 138 LEU CD2 HD21 sing N N 139 LEU CD2 HD22 sing N N 140 LEU CD2 HD23 sing N N 141 LEU OXT HXT sing N N 142 # _pdbx_audit_support.funding_organization 'Research Foundation - Flanders (FWO)' _pdbx_audit_support.country Belgium _pdbx_audit_support.grant_number 'EOS project G0G3118N (EOS ID 30650620)' _pdbx_audit_support.ordinal 1 # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'AVACE II' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 700 _pdbx_nmr_spectrometer.details 'Prodigy Cryoprobe' # _atom_sites.entry_id 9EPS _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _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 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C H N O # loop_ #