data_5ZYX # _entry.id 5ZYX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.370 _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 5ZYX pdb_00005zyx 10.2210/pdb5zyx/pdb WWPDB D_1300007882 ? ? BMRB 36191 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Solution NMR structure of K30 peptide in 10 mM dioctanoyl phosphatidylglycerol (D8PG)' _pdbx_database_related.db_id 36191 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 5ZYX _pdbx_database_status.recvd_initial_deposition_date 2018-05-28 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Bhunia, A.' 1 ? 'Mohid, A.' 2 ? 'Stella, L.' 3 ? 'Calligari, P.' 4 ? # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Bioconjug.Chem. _citation.journal_id_ASTM BCCHES _citation.journal_id_CSD 2063 _citation.journal_id_ISSN 1043-1802 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 30 _citation.language ? _citation.page_first 1998 _citation.page_last 2010 _citation.title ;Design, Synthesis, Antibacterial Potential, and Structural Characterization of N-Acylated Derivatives of the Human Autophagy 16 Polypeptide. ; _citation.year 2019 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.bioconjchem.9b00290 _citation.pdbx_database_id_PubMed 31145591 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Varnava, K.G.' 1 ? primary 'Mohid, S.A.' 2 ? primary 'Calligari, P.' 3 ? primary 'Stella, L.' 4 ? primary 'Reynison, J.' 5 ? primary 'Bhunia, A.' 6 ? primary 'Sarojini, V.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ARG-TRP-LYS-ARG-HIS-ILE-SER-GLU-GLN-LEU-ARG-ARG-ARG-ASP-ARG-LEU-GLN-ARG-GLN-ALA _entity.formula_weight 2698.125 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 RWKRHISEQLRRRDRLQRQA _entity_poly.pdbx_seq_one_letter_code_can RWKRHISEQLRRRDRLQRQA _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 TRP n 1 3 LYS n 1 4 ARG n 1 5 HIS n 1 6 ILE n 1 7 SER n 1 8 GLU n 1 9 GLN n 1 10 LEU n 1 11 ARG n 1 12 ARG n 1 13 ARG n 1 14 ASP n 1 15 ARG n 1 16 LEU n 1 17 GLN n 1 18 ARG n 1 19 GLN n 1 20 ALA 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 20 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5ZYX _struct_ref.pdbx_db_accession 5ZYX _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 5ZYX _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 20 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5ZYX _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 20 _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 20 # 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 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 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 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 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 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 # 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 TOCSY' 1 isotropic 2 1 1 '2D 1H-1H NOESY' 1 isotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure_units bar _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 4.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units 'Not defined' _pdbx_nmr_exptl_sample_conditions.label 'Solution in water' _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 # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '1 mM 1H K30 Peptide, 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 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'AVANCE III' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.details ? # _pdbx_nmr_refine.entry_id 5ZYX _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 3 # _pdbx_nmr_ensemble.entry_id 5ZYX _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.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 5ZYX _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 processing TopSpin ? 'Bruker Biospin' 2 'chemical shift assignment' Sparky ? Goddard 3 'structure calculation' CYANA ? 'Guntert, Mumenthaler and Wuthrich' 4 collection TopSpin ? 'Bruker Biospin' # _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 5ZYX _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 5ZYX _struct.title 'Solution NMR structure of K30 peptide in 10 mM dioctanoyl phosphatidylglycerol (D8PG)' _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 5ZYX _struct_keywords.text 'STRUCTURE FROM CYANA 2.1, K30, D8PG, ANTIMICROBIAL PROTEIN' _struct_keywords.pdbx_keywords '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 ? # 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 AA1 ARG A 1 ? ARG A 13 ? ARG A 1 ARG A 13 1 ? 13 HELX_P HELX_P2 AA2 ASP A 14 ? ALA A 20 ? ASP A 14 ALA A 20 1 ? 7 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 5ZYX _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 TRP 2 2 2 TRP TRP A . n A 1 3 LYS 3 3 3 LYS LYS A . n A 1 4 ARG 4 4 4 ARG ARG A . n A 1 5 HIS 5 5 5 HIS HIS A . n A 1 6 ILE 6 6 6 ILE ILE A . n A 1 7 SER 7 7 7 SER SER A . n A 1 8 GLU 8 8 8 GLU GLU A . n A 1 9 GLN 9 9 9 GLN GLN A . n A 1 10 LEU 10 10 10 LEU LEU A . n A 1 11 ARG 11 11 11 ARG ARG A . n A 1 12 ARG 12 12 12 ARG ARG A . n A 1 13 ARG 13 13 13 ARG ARG A . n A 1 14 ASP 14 14 14 ASP ASP A . n A 1 15 ARG 15 15 15 ARG ARG A . n A 1 16 LEU 16 16 16 LEU LEU A . n A 1 17 GLN 17 17 17 GLN GLN A . n A 1 18 ARG 18 18 18 ARG ARG A . n A 1 19 GLN 19 19 19 GLN GLN A . n A 1 20 ALA 20 20 20 ALA ALA 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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 2670 ? # _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 ? _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 2019-06-12 2 'Structure model' 1 1 2019-06-19 3 'Structure model' 1 2 2019-07-10 4 'Structure model' 1 3 2019-07-31 5 'Structure model' 1 4 2023-06-14 # _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 ? # 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' 'Data collection' 2 2 'Structure model' 'Structure summary' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 5 'Structure model' 'Database references' 8 5 'Structure model' Other # 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' audit_author 2 2 'Structure model' pdbx_nmr_spectrometer 3 3 'Structure model' citation 4 3 'Structure model' citation_author 5 4 'Structure model' citation 6 4 'Structure model' citation_author 7 5 'Structure model' database_2 8 5 'Structure model' pdbx_database_status # 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' '_pdbx_nmr_spectrometer.model' 2 3 'Structure model' '_citation.title' 3 3 'Structure model' '_citation_author.identifier_ORCID' 4 3 'Structure model' '_citation_author.name' 5 4 'Structure model' '_citation.journal_volume' 6 4 'Structure model' '_citation.page_first' 7 4 'Structure model' '_citation.page_last' 8 4 'Structure model' '_citation_author.identifier_ORCID' 9 5 'Structure model' '_database_2.pdbx_DOI' 10 5 'Structure model' '_database_2.pdbx_database_accession' 11 5 'Structure model' '_pdbx_database_status.status_code_nmr_data' # _pdbx_nmr_exptl_sample.solution_id 1 _pdbx_nmr_exptl_sample.component 'K30 Peptide' _pdbx_nmr_exptl_sample.concentration 1 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling 1H # 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 ARG A 12 ? ? -98.27 -72.39 2 3 ARG A 12 ? ? -94.20 -67.14 3 4 ARG A 12 ? ? -94.63 -66.58 4 6 ARG A 12 ? ? -94.65 -66.84 5 8 ARG A 12 ? ? -113.19 -70.48 6 9 ARG A 12 ? ? -114.05 -70.12 7 11 ARG A 12 ? ? -95.28 -66.23 8 12 ARG A 12 ? ? -105.21 -66.56 9 15 ARG A 12 ? ? -96.22 -67.53 10 16 ARG A 12 ? ? -75.20 -102.41 11 17 ARG A 12 ? ? -74.92 -102.58 12 18 ARG A 12 ? ? -75.24 -102.24 13 19 ARG A 12 ? ? -71.15 -103.28 14 20 ARG A 12 ? ? -51.34 -83.03 15 20 ARG A 13 ? ? -122.82 -117.71 16 20 ARG A 15 ? ? -85.39 -82.73 # _pdbx_audit_support.funding_organization ? _pdbx_audit_support.country India _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'mass spectrometry' _pdbx_struct_assembly_auth_evidence.details ? #