data_2MMT # _entry.id 2MMT # _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 2MMT RCSB RCSB103802 BMRB 19865 WWPDB D_1000103802 # _pdbx_database_related.db_id 19865 _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2MMT _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-03-18 _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 # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hegemann, J.D.' 1 'Zimmermann, M.' 2 'Knappe, T.A.' 3 'Xie, X.' 4 'Marahiel, M.A.' 5 # _citation.id primary _citation.title 'Rational improvement of the affinity and selectivity of integrin binding of grafted lasso peptides.' _citation.journal_abbrev J.Med.Chem. _citation.journal_volume 57 _citation.page_first 5829 _citation.page_last 5834 _citation.year 2014 _citation.journal_id_ASTM JMCMAR _citation.country US _citation.journal_id_ISSN 0022-2623 _citation.journal_id_CSD 0151 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24949551 _citation.pdbx_database_id_DOI 10.1021/jm5004478 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Hegemann, J.D.' 1 primary 'De Simone, M.' 2 primary 'Zimmermann, M.' 3 primary 'Knappe, T.A.' 4 primary 'Xie, X.' 5 primary 'Di Leva, F.S.' 6 primary 'Marinelli, L.' 7 primary 'Novellino, E.' 8 primary 'Zahler, S.' 9 primary 'Kessler, H.' 10 primary 'Marahiel, M.A.' 11 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Microcin J25 RGDF mutant' _entity.formula_weight 2274.490 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation G12R/I13G/G14D/T15F _entity.pdbx_fragment 'UNP residues 38-58' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'MccJ25(RGDF)' # _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 GGAGHVPEYFVRGDFPISFYG _entity_poly.pdbx_seq_one_letter_code_can GGAGHVPEYFVRGDFPISFYG _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 GLY n 1 2 GLY n 1 3 ALA n 1 4 GLY n 1 5 HIS n 1 6 VAL n 1 7 PRO n 1 8 GLU n 1 9 TYR n 1 10 PHE n 1 11 VAL n 1 12 ARG n 1 13 GLY n 1 14 ASP n 1 15 PHE n 1 16 PRO n 1 17 ILE n 1 18 SER n 1 19 PHE n 1 20 TYR n 1 21 GLY 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 'Escherichia coli' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 562 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code MCJA_ECOLX _struct_ref.pdbx_db_accession Q9X2V7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GGAGHVPEYFVGIGTPISFYG _struct_ref.pdbx_align_begin 38 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2MMT _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 21 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9X2V7 _struct_ref_seq.db_align_beg 38 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 58 _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 21 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 2MMT ARG A 12 ? UNP Q9X2V7 GLY 49 'ENGINEERED MUTATION' 12 1 1 2MMT GLY A 13 ? UNP Q9X2V7 ILE 50 'ENGINEERED MUTATION' 13 2 1 2MMT ASP A 14 ? UNP Q9X2V7 GLY 51 'ENGINEERED MUTATION' 14 3 1 2MMT PHE A 15 ? UNP Q9X2V7 THR 52 'ENGINEERED MUTATION' 15 4 # 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 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 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 DQF-COSY' 1 2 1 '2D 1H-1H TOCSY' 1 3 1 '2D 1H-1H NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH . _pdbx_nmr_exptl_sample_conditions.pressure 1.0 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '12.6 mM MCCJ25(RGDF), methanol' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system methanol # _pdbx_nmr_spectrometer.field_strength 600 _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 2MMT _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 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 15 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2MMT _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 2MMT _pdbx_nmr_representative.selection_criteria 'lowest energy' # _pdbx_nmr_software.authors 'Guntert, Mumenthaler' _pdbx_nmr_software.classification refinement _pdbx_nmr_software.name CYANA _pdbx_nmr_software.version 2.1 _pdbx_nmr_software.ordinal 1 # _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 2MMT _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2MMT _struct.title 'Lasso peptide-based integrin inhibitor: Microcin J25 variant with RGDF substitution of Gly12-Ile13-Gly14-Thr15' _struct.pdbx_descriptor 'Microcin J25' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2MMT _struct_keywords.pdbx_keywords ANTIBIOTIC _struct_keywords.text 'lasso peptide, epitope grafting, integrin inhibitor, drug design, molecular scaffolds, molecular dynamics, ANTIBIOTIC' # _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 ? # _struct_conn.id covale1 _struct_conn.conn_type_id covale _struct_conn.pdbx_leaving_atom_flag ? _struct_conn.pdbx_PDB_id ? _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_comp_id GLY _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_label_atom_id N _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 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_comp_id GLU _struct_conn.ptnr2_label_seq_id 8 _struct_conn.ptnr2_label_atom_id CD _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id GLY _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id GLU _struct_conn.ptnr2_auth_seq_id 8 _struct_conn.ptnr2_symmetry 1_555 _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 1.354 _struct_conn.pdbx_value_order ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2MMT _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 GLY 1 1 1 GLY GLY A . n A 1 2 GLY 2 2 2 GLY GLY A . n A 1 3 ALA 3 3 3 ALA ALA A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 HIS 5 5 5 HIS HIS A . n A 1 6 VAL 6 6 6 VAL VAL A . n A 1 7 PRO 7 7 7 PRO PRO A . n A 1 8 GLU 8 8 8 GLU GLU A . n A 1 9 TYR 9 9 9 TYR TYR A . n A 1 10 PHE 10 10 10 PHE PHE A . n A 1 11 VAL 11 11 11 VAL VAL A . n A 1 12 ARG 12 12 12 ARG ARG A . n A 1 13 GLY 13 13 13 GLY GLY A . n A 1 14 ASP 14 14 14 ASP ASP A . n A 1 15 PHE 15 15 15 PHE PHE A . n A 1 16 PRO 16 16 16 PRO PRO A . n A 1 17 ILE 17 17 17 ILE ILE A . n A 1 18 SER 18 18 18 SER SER A . n A 1 19 PHE 19 19 19 PHE PHE A . n A 1 20 TYR 20 20 20 TYR TYR A . n A 1 21 GLY 21 21 21 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 2014-07-02 2 'Structure model' 1 1 2014-07-23 # _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_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' # _pdbx_nmr_exptl_sample.component 'MCCJ25(RGDF)-1' _pdbx_nmr_exptl_sample.concentration 12.6 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling ? _pdbx_nmr_exptl_sample.solution_id 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 12 ? ? -76.74 29.51 2 1 ASP A 14 ? ? -116.11 -76.10 3 2 ARG A 12 ? ? -76.92 29.41 4 2 ASP A 14 ? ? -115.96 -76.24 5 2 ILE A 17 ? ? -103.10 -64.41 6 3 ALA A 3 ? ? -108.20 42.04 7 3 ARG A 12 ? ? -76.83 29.91 8 3 ASP A 14 ? ? -116.26 -75.34 9 3 ILE A 17 ? ? -102.86 -64.54 10 3 TYR A 20 ? ? -69.39 -178.36 11 4 ALA A 3 ? ? -108.61 43.49 12 4 ARG A 12 ? ? -77.06 29.36 13 4 ASP A 14 ? ? -116.10 -75.74 14 4 ILE A 17 ? ? -102.39 -64.88 15 5 ARG A 12 ? ? -77.23 25.10 16 5 ASP A 14 ? ? -116.06 -76.43 17 5 ILE A 17 ? ? -102.07 -64.69 18 6 ARG A 12 ? ? -76.97 26.23 19 6 ASP A 14 ? ? -116.27 -76.09 20 6 ILE A 17 ? ? -100.64 -63.98 21 7 ALA A 3 ? ? -105.20 45.44 22 7 ARG A 12 ? ? -77.16 25.68 23 7 ASP A 14 ? ? -116.18 -76.22 24 7 TYR A 20 ? ? -68.77 -174.24 25 8 ARG A 12 ? ? -77.25 25.16 26 8 ASP A 14 ? ? -116.10 -76.63 27 8 ILE A 17 ? ? -108.36 -63.67 28 9 ARG A 12 ? ? -77.21 25.30 29 9 ASP A 14 ? ? -116.24 -76.24 30 10 ARG A 12 ? ? -77.47 25.15 31 10 ASP A 14 ? ? -116.13 -76.18 32 10 ILE A 17 ? ? -105.64 -61.27 33 11 ARG A 12 ? ? -76.64 29.64 34 11 ASP A 14 ? ? -116.10 -75.49 35 11 ILE A 17 ? ? -107.35 -60.57 36 12 ARG A 12 ? ? -76.83 25.85 37 12 ASP A 14 ? ? -116.30 -76.20 38 13 ARG A 12 ? ? -76.88 25.78 39 13 ASP A 14 ? ? -116.15 -76.24 40 13 ILE A 17 ? ? -100.00 -61.75 41 14 ARG A 12 ? ? -77.20 25.82 42 14 ASP A 14 ? ? -116.25 -76.00 43 15 ALA A 3 ? ? -107.39 43.22 44 15 ARG A 12 ? ? -76.90 25.71 45 15 ASP A 14 ? ? -116.06 -76.15 46 15 ILE A 17 ? ? -107.80 -62.95 47 15 TYR A 20 ? ? -67.77 -177.09 #