data_2MXH # _entry.id 2MXH # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_code _database_2.database_id _database_2.pdbx_database_accession _database_2.pdbx_DOI RCSB104166 RCSB ? ? 2MXH PDB pdb_00002mxh 10.2210/pdb2mxh/pdb 25409 BMRB ? ? D_1000104166 WWPDB ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 2MXG PDB unspecified 'structure of VG16KRKP, an antimicrobial peptide in D8PG micelles' 25409 BMRB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2MXH _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2015-01-01 _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.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 'Bhunia, A.' 1 'Datta, A.' 2 # _citation.id primary _citation.title ;De-novo design of antimicrobial peptides:insights into membrane permeabilisation, lipopolysachharide fragmentation and application in plant disease control ; _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bhunia, A.' 1 ? primary 'Datta, A.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'antimicrobial peptide' _entity.formula_weight 1765.157 _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 VARGWKRKCPLFGKGG _entity_poly.pdbx_seq_one_letter_code_can VARGWKRKCPLFGKGG _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 VAL n 1 2 ALA n 1 3 ARG n 1 4 GLY n 1 5 TRP n 1 6 LYS n 1 7 ARG n 1 8 LYS n 1 9 CYS n 1 10 PRO n 1 11 LEU n 1 12 PHE n 1 13 GLY n 1 14 LYS n 1 15 GLY n 1 16 GLY n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2MXH _struct_ref.pdbx_db_accession 2MXH _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2MXH _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 16 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2MXH _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 16 _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 16 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 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 NOESY' 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 ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 308 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '0.5 mM antimicrobial peptide, 55.55 M H2O, 200 mM SDS, 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 500 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2MXH _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _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 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2MXH _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.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2MXH _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Guntert, Mumenthaler and Wuthrich' 'structure solution' CYANA ? 1 'Guntert, Mumenthaler and Wuthrich' refinement CYANA ? 2 # _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 2MXH _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2MXH _struct.title 'NMR resolved structure of VG16KRKP, an antimicrobial peptide in SDS' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2MXH _struct_keywords.pdbx_keywords 'ANTIMICROBIAL PROTEIN' _struct_keywords.text 'turn, short helical segment, 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 ARG A 3 ? LYS A 8 ? ARG A 3 LYS A 8 1 ? 6 HELX_P HELX_P2 2 CYS A 9 ? LYS A 14 ? CYS A 9 LYS A 14 5 ? 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 2MXH _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 VAL 1 1 1 VAL VAL A . n A 1 2 ALA 2 2 2 ALA ALA A . n A 1 3 ARG 3 3 3 ARG ARG A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 TRP 5 5 5 TRP TRP A . n A 1 6 LYS 6 6 6 LYS LYS A . n A 1 7 ARG 7 7 7 ARG ARG A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 CYS 9 9 9 CYS CYS A . n A 1 10 PRO 10 10 10 PRO PRO 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 GLY 13 13 13 GLY GLY A . n A 1 14 LYS 14 14 14 LYS LYS A . n A 1 15 GLY 15 15 15 GLY GLY A . n A 1 16 GLY 16 16 16 GLY GLY 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 2015-02-04 2 'Structure model' 1 1 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' 'Database references' 3 2 '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' database_2 2 2 'Structure model' pdbx_database_status 3 2 'Structure model' pdbx_nmr_spectrometer # 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' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 2 'Structure model' '_pdbx_nmr_spectrometer.model' # loop_ _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 _pdbx_nmr_exptl_sample.solution_id 'antimicrobial peptide-1' 0.5 ? mM ? 1 H2O-2 55.55 ? M ? 1 SDS-3 200 ? mM ? 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 ARG A 7 ? ? -64.67 -83.53 2 1 LYS A 8 ? ? -96.39 -77.20 3 2 ALA A 2 ? ? -103.02 43.33 4 2 ARG A 7 ? ? -75.42 -76.51 5 2 LYS A 8 ? ? -93.29 -81.05 6 3 ALA A 2 ? ? -119.98 55.47 7 3 ARG A 7 ? ? -82.29 -81.24 8 3 LYS A 8 ? ? -98.57 -80.33 9 4 ALA A 2 ? ? -114.61 64.75 10 4 ARG A 7 ? ? -65.04 -83.19 11 4 LYS A 8 ? ? -96.27 -77.21 12 4 PHE A 12 ? ? -85.18 46.18 13 5 ARG A 7 ? ? -71.49 -80.50 14 5 LYS A 8 ? ? -99.04 -79.89 15 5 PHE A 12 ? ? -88.91 40.04 16 6 ALA A 2 ? ? -119.62 71.97 17 6 ARG A 7 ? ? -71.14 -79.14 18 6 LYS A 8 ? ? -94.09 -78.15 19 7 ARG A 7 ? ? -60.84 -82.96 20 7 LYS A 8 ? ? -96.00 -77.91 21 7 PHE A 12 ? ? -88.32 38.79 22 8 ALA A 2 ? ? -95.76 57.62 23 8 ARG A 7 ? ? -79.08 -85.98 24 8 LYS A 8 ? ? -98.11 -77.80 25 8 PHE A 12 ? ? -80.85 47.58 26 9 ARG A 7 ? ? -63.45 -82.57 27 9 LYS A 8 ? ? -97.68 -77.79 28 9 PHE A 12 ? ? -86.76 44.91 29 10 ALA A 2 ? ? -116.29 66.44 30 10 ARG A 7 ? ? -65.67 -83.06 31 10 LYS A 8 ? ? -98.36 -77.15 32 11 ALA A 2 ? ? -102.05 68.83 33 11 LYS A 8 ? ? -80.23 -75.75 34 11 LYS A 14 ? ? -96.28 -75.88 35 12 ALA A 2 ? ? -107.15 61.98 36 12 ARG A 7 ? ? -73.08 -77.95 37 12 LYS A 8 ? ? -97.20 -80.14 38 13 ARG A 7 ? ? -60.70 -83.70 39 13 LYS A 8 ? ? -96.63 -77.64 40 13 LYS A 14 ? ? -63.54 -75.53 41 14 LYS A 8 ? ? -90.47 -76.04 42 14 LYS A 14 ? ? -101.86 -73.32 43 15 TRP A 5 ? ? -37.12 -77.49 44 15 ARG A 7 ? ? -55.53 -78.70 45 15 LYS A 8 ? ? -96.61 -78.40 46 15 PHE A 12 ? ? -90.62 39.76 47 16 TRP A 5 ? ? -41.85 -76.11 48 16 ARG A 7 ? ? -74.91 -79.29 49 16 LYS A 8 ? ? -93.06 -75.95 50 17 TRP A 5 ? ? -36.56 -77.48 51 17 ARG A 7 ? ? -55.26 -78.52 52 17 LYS A 8 ? ? -96.59 -78.49 53 18 ALA A 2 ? ? -108.32 59.68 54 18 ARG A 7 ? ? -65.28 -82.76 55 18 LYS A 8 ? ? -98.38 -77.64 56 18 LYS A 14 ? ? -120.12 -68.55 57 19 ARG A 7 ? ? -80.20 -85.55 58 19 LYS A 8 ? ? -102.96 -80.20 59 19 CYS A 9 ? ? -53.55 109.12 60 20 ALA A 2 ? ? -95.86 54.93 61 20 ARG A 7 ? ? -78.92 -82.32 62 20 LYS A 8 ? ? -102.25 -80.37 #