data_2MQ5 # _entry.id 2MQ5 # _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_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2MQ5 pdb_00002mq5 10.2210/pdb2mq5/pdb RCSB RCSB103917 ? ? BMRB 25012 ? ? WWPDB D_1000103917 ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 25012 BMRB unspecified . 2MQ2 PDB unspecified . 2MQ4 PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2MQ5 _pdbx_database_status.methods_development_category ? _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2014-06-12 _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.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mohanram, H.' 1 'Bhattacharjya, S.' 2 # _citation.id primary _citation.title 'Cysteine deleted protegrin-1 (CDP-1): anti-bacterial activity, outer-membrane disruption and selectivity.' _citation.journal_abbrev Biochim.Biophys.Acta _citation.journal_volume 1840 _citation.page_first 3006 _citation.page_last 3016 _citation.year 2014 _citation.journal_id_ASTM BBACAQ _citation.country NE _citation.journal_id_ISSN 0006-3002 _citation.journal_id_CSD 0113 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24997421 _citation.pdbx_database_id_DOI 10.1016/j.bbagen.2014.06.018 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mohanram, H.' 1 ? primary 'Bhattacharjya, S.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'LR10 peptide from Cysteine Deleted Protegrin-1' _entity.formula_weight 1325.609 _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 LYRRRFVVGR _entity_poly.pdbx_seq_one_letter_code_can LYRRRFVVGR _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 LEU n 1 2 TYR n 1 3 ARG n 1 4 ARG n 1 5 ARG n 1 6 PHE n 1 7 VAL n 1 8 VAL n 1 9 GLY n 1 10 ARG n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2MQ5 _struct_ref.pdbx_db_accession 2MQ5 _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 2MQ5 _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 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2MQ5 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _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 10 # 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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.solution_id 1 _pdbx_nmr_exptl.type '2D 1H-1H NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 55.1 _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 278 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '55.1 M protein-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 2MQ5 _pdbx_nmr_refine.method 'simulated annealing' _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 2MQ5 _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 2MQ5 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.ordinal _pdbx_nmr_software.version Goddard 'chemical shift assignment' Sparky 1 ? Goddard refinement Sparky 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 2MQ5 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2MQ5 _struct.title 'Cysteine Deleted Protegrin-1 (CDP-1): Anti-bacterial Activity, Outer-Membrane Disruption and Selectivity' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2MQ5 _struct_keywords.pdbx_keywords 'ANTIMICROBIAL PROTEIN' _struct_keywords.text 'random coil, 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 ? # _atom_sites.entry_id 2MQ5 _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 LEU 1 1 1 LEU LEU A . n A 1 2 TYR 2 2 2 TYR TYR A . n A 1 3 ARG 3 3 3 ARG ARG A . n A 1 4 ARG 4 4 4 ARG ARG A . n A 1 5 ARG 5 5 5 ARG ARG A . n A 1 6 PHE 6 6 6 PHE PHE A . n A 1 7 VAL 7 7 7 VAL VAL A . n A 1 8 VAL 8 8 8 VAL VAL A . n A 1 9 GLY 9 9 9 GLY GLY A . n A 1 10 ARG 10 10 10 ARG ARG 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 2014-07-30 2 'Structure model' 1 1 2022-08-24 3 'Structure model' 1 2 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 3 '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' citation 2 2 'Structure model' database_2 3 2 'Structure model' pdbx_nmr_software 4 3 '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' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.title' 5 2 'Structure model' '_database_2.pdbx_DOI' 6 2 'Structure model' '_database_2.pdbx_database_accession' 7 2 'Structure model' '_pdbx_nmr_software.name' 8 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' # _pdbx_nmr_exptl_sample.component protein-1 _pdbx_nmr_exptl_sample.concentration 55.1 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units M _pdbx_nmr_exptl_sample.isotopic_labeling ? _pdbx_nmr_exptl_sample.solution_id 1 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 2 2 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 3 3 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 4 4 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 5 5 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 6 6 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 7 7 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 8 8 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 9 9 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 10 10 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 11 11 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 12 12 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 13 13 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 14 14 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 15 15 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 16 16 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 17 17 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 18 18 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 19 19 O A PHE 6 ? ? N A VAL 8 ? ? 2.02 # 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 TYR A 2 ? ? -123.01 -94.33 2 1 ARG A 3 ? ? -178.15 16.11 3 1 VAL A 7 ? ? 11.54 43.08 4 1 VAL A 8 ? ? -59.62 14.22 5 2 TYR A 2 ? ? -123.05 -94.46 6 2 ARG A 3 ? ? -178.22 17.05 7 2 VAL A 7 ? ? 11.49 43.07 8 2 VAL A 8 ? ? -59.68 14.49 9 3 TYR A 2 ? ? -123.03 -94.31 10 3 ARG A 3 ? ? -178.08 16.10 11 3 VAL A 7 ? ? 11.54 43.08 12 3 VAL A 8 ? ? -59.69 14.48 13 4 TYR A 2 ? ? -123.01 -94.83 14 4 ARG A 3 ? ? -177.54 16.97 15 4 VAL A 7 ? ? 11.55 43.02 16 4 VAL A 8 ? ? -59.57 14.18 17 5 TYR A 2 ? ? -122.21 -93.90 18 5 ARG A 3 ? ? -178.10 15.87 19 5 VAL A 7 ? ? 11.54 42.99 20 5 VAL A 8 ? ? -59.54 14.17 21 6 TYR A 2 ? ? -122.19 -94.24 22 6 ARG A 3 ? ? -178.00 15.41 23 6 VAL A 7 ? ? 11.58 42.95 24 6 VAL A 8 ? ? -59.55 14.26 25 7 TYR A 2 ? ? -122.84 -94.89 26 7 ARG A 3 ? ? -177.56 16.40 27 7 VAL A 7 ? ? 11.59 43.02 28 7 VAL A 8 ? ? -59.69 14.53 29 8 TYR A 2 ? ? -123.14 -94.91 30 8 ARG A 3 ? ? -178.58 16.42 31 8 VAL A 7 ? ? 11.42 43.17 32 8 VAL A 8 ? ? -59.50 14.16 33 9 TYR A 2 ? ? -123.08 -94.56 34 9 ARG A 3 ? ? -178.20 16.95 35 9 VAL A 7 ? ? 11.56 43.05 36 9 VAL A 8 ? ? -59.68 14.44 37 10 TYR A 2 ? ? -122.98 -94.71 38 10 ARG A 3 ? ? -177.51 16.51 39 10 VAL A 7 ? ? 11.60 42.99 40 10 VAL A 8 ? ? -59.79 15.15 41 11 TYR A 2 ? ? -123.22 -95.03 42 11 ARG A 3 ? ? 178.85 22.32 43 11 VAL A 7 ? ? 11.46 43.06 44 11 VAL A 8 ? ? -59.56 14.24 45 12 TYR A 2 ? ? -121.93 -97.33 46 12 ARG A 3 ? ? -176.35 28.47 47 12 VAL A 7 ? ? 11.53 43.08 48 12 VAL A 8 ? ? -59.65 14.34 49 13 TYR A 2 ? ? -122.02 -94.15 50 13 ARG A 3 ? ? 177.18 22.82 51 13 VAL A 7 ? ? 11.47 43.10 52 13 VAL A 8 ? ? -59.59 14.20 53 14 TYR A 2 ? ? -122.83 -94.73 54 14 ARG A 3 ? ? -177.41 14.20 55 14 VAL A 7 ? ? 11.54 43.04 56 14 VAL A 8 ? ? -59.57 14.15 57 15 TYR A 2 ? ? -122.92 -95.93 58 15 ARG A 3 ? ? -178.09 19.30 59 15 VAL A 7 ? ? 11.55 43.02 60 15 VAL A 8 ? ? -59.52 14.23 61 16 TYR A 2 ? ? -122.91 -95.95 62 16 ARG A 3 ? ? -178.12 19.43 63 16 VAL A 7 ? ? 11.49 43.09 64 16 VAL A 8 ? ? -59.66 14.27 65 17 TYR A 2 ? ? -122.98 -98.59 66 17 ARG A 3 ? ? -160.24 5.53 67 17 VAL A 7 ? ? 11.66 42.90 68 17 VAL A 8 ? ? -59.57 14.05 69 18 TYR A 2 ? ? -122.76 -98.83 70 18 ARG A 3 ? ? -161.74 7.12 71 18 VAL A 7 ? ? 11.51 43.01 72 18 VAL A 8 ? ? -59.85 15.13 73 19 TYR A 2 ? ? -124.99 -87.90 74 19 ARG A 3 ? ? 177.11 11.41 75 19 VAL A 7 ? ? 11.54 43.02 76 19 VAL A 8 ? ? -59.47 14.04 77 20 TYR A 2 ? ? -121.08 -84.07 78 20 ARG A 3 ? ? -177.05 24.00 79 20 PHE A 6 ? ? -120.86 -131.46 80 20 VAL A 8 ? ? -58.56 15.98 #