data_5M2K # _entry.id 5M2K # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5M2K WWPDB D_1200001800 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5M2K _pdbx_database_status.recvd_initial_deposition_date 2016-10-13 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zarkan, A.' 1 'Macklyne, H.-R.' 2 'Chirgadze, D.Y.' 3 'Bond, A.D.' 4 'Hesketh, A.R.' 5 'Hong, H.-J.' 6 # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Sci Rep' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2045-2322 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 7 _citation.language ? _citation.page_first 4893 _citation.page_last 4893 _citation.title 'Zn(II) mediates vancomycin polymerization and potentiates its antibiotic activity against resistant bacteria.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41598-017-04868-2 _citation.pdbx_database_id_PubMed 28687742 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zarkan, A.' 1 ? primary 'Macklyne, H.R.' 2 ? primary 'Chirgadze, D.Y.' 3 ? primary 'Bond, A.D.' 4 ? primary 'Hesketh, A.R.' 5 ? primary 'Hong, H.J.' 6 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 5M2K _cell.details ? _cell.formula_units_Z ? _cell.length_a 35.899 _cell.length_a_esd ? _cell.length_b 35.899 _cell.length_b_esd ? _cell.length_c 55.553 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 18 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M2K _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? # 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 vancomycin 1149.977 2 ? ? ? ? 2 branched man 'vancosamine-(1-2)-beta-D-glucopyranose' 323.340 2 ? ? ? ? 3 non-polymer syn 1,2-ETHANEDIOL 62.068 2 ? ? ? ? 4 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ? 5 water nat water 18.015 63 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(MLU)(OMZ)N(GHP)(GHP)(OMY)(3FG)' _entity_poly.pdbx_seq_one_letter_code_can XXNGGYX _entity_poly.pdbx_strand_id A,B _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 MLU n 1 2 OMZ n 1 3 ASN n 1 4 GHP n 1 5 GHP n 1 6 OMY n 1 7 3FG 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 7 _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Amycolatopsis orientalis' _entity_src_nat.pdbx_ncbi_taxonomy_id 31958 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _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 ? # _struct_ref.id 1 _struct_ref.db_name NOR _struct_ref.db_code 5M2K _struct_ref.pdbx_db_accession NOR00681 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 5M2K A 1 ? 7 ? 5M2K 1 ? 7 ? 1 7 2 1 5M2K B 1 ? 7 ? 5M2K 1 ? 7 ? 1 7 # 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 3FG 'L-peptide linking' . '(2S)-amino(3,5-dihydroxyphenyl)ethanoic acid' ? 'C8 H9 N O4' 183.161 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 BGC 'D-saccharide, beta linking' . beta-D-glucopyranose ? 'C6 H12 O6' 180.156 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 GHP 'D-peptide linking' . '(2R)-amino(4-hydroxyphenyl)ethanoic acid' ? 'C8 H9 N O3' 167.162 HOH non-polymer . WATER ? 'H2 O' 18.015 MLU 'D-peptide linking' . N-methyl-D-leucine ? 'C7 H15 N O2' 145.199 OMY 'L-peptide linking' n '(betaR)-3-chloro-beta-hydroxy-L-tyrosine' ? 'C9 H10 Cl N O4' 231.633 OMZ 'D-peptide linking' . '(betaR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE' ? 'C9 H10 Cl N O4' 231.633 RER 'L-saccharide, alpha linking' . vancosamine VANCOSAMINE 'C7 H15 N O3' 161.199 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # _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 5M2K _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 3.00 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 58.94 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 292 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.2 M magnesium formate salt, 20% (w/v) PEG 3350' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-01-14 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.92819 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'DIAMOND BEAMLINE I04-1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.92819 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I04-1 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5M2K _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.00 _reflns.d_resolution_low 27.13 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 14362 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 96.3 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 8.1 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 27 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.00 _reflns_shell.d_res_low 1.05 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 13.7 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 81.9 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.137 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 4.3 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] 0.0000 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][2] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.aniso_B[3][3] 0.0100 _refine.B_iso_max 70.910 _refine.B_iso_mean 8.1520 _refine.B_iso_min 2.000 _refine.correlation_coeff_Fo_to_Fc 0.9770 _refine.correlation_coeff_Fo_to_Fc_free 0.9740 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 5M2K _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.0000 _refine.ls_d_res_low 27.1300 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 12922 _refine.ls_number_reflns_R_free 1440 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.5300 _refine.ls_percent_reflns_R_free 10.0000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.0976 _refine.ls_R_factor_R_free 0.1045 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.0968 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.0160 _refine.pdbx_overall_ESU_R_Free 0.0160 _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B 0.2750 _refine.overall_SU_ML 0.0070 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.0000 _refine_hist.d_res_low 27.1300 _refine_hist.pdbx_number_atoms_ligand 51 _refine_hist.number_atoms_solvent 63 _refine_hist.number_atoms_total 274 _refine_hist.pdbx_number_residues_total 14 _refine_hist.pdbx_B_iso_mean_ligand 8.52 _refine_hist.pdbx_B_iso_mean_solvent 21.60 _refine_hist.pdbx_number_atoms_protein 160 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.038 0.020 226 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.018 0.020 162 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 2.307 2.806 296 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 5.195 3.000 354 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? 12.455 5.000 8 ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? 54.080 30.000 2 ? r_dihedral_angle_2_deg ? ? 'X-RAY DIFFRACTION' ? 20.305 15.000 2 ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? 0.179 0.200 36 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.038 0.020 192 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.010 0.020 52 ? r_gen_planes_other ? ? 'X-RAY DIFFRACTION' ? 0.552 0.403 54 ? r_mcbond_it ? ? 'X-RAY DIFFRACTION' ? 0.545 0.403 53 ? r_mcbond_other ? ? 'X-RAY DIFFRACTION' ? 0.561 0.604 52 ? r_mcangle_it ? ? 'X-RAY DIFFRACTION' ? 6.430 3.000 388 ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? 28.441 5.000 13 ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? 7.306 5.000 423 ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.0000 _refine_ls_shell.d_res_low 1.0260 _refine_ls_shell.number_reflns_all 1035 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 104 _refine_ls_shell.number_reflns_R_work 931 _refine_ls_shell.percent_reflns_obs 97.0000 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.0820 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.0720 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 5M2K _struct.title 'Crystal structure of vancomycin-Zn(II) complex' _struct.pdbx_descriptor vancomycin _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 5M2K _struct_keywords.text 'vancomycin, zinc, glycopeptide, antibiotic' _struct_keywords.pdbx_keywords ANTIBIOTIC # 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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 4 ? G N N 3 ? H N N 5 ? I N N 5 ? # 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 MLU 1 C ? ? ? 1_555 A OMZ 2 N ? ? A MLU 1 A OMZ 2 1_555 ? ? ? ? ? ? ? 1.358 ? ? covale2 covale both ? A OMZ 2 C ? ? ? 1_555 A ASN 3 N ? ? A OMZ 2 A ASN 3 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale3 covale none ? A OMZ 2 OH ? ? ? 1_555 A GHP 4 C5 ? ? A OMZ 2 A GHP 4 1_555 ? ? ? ? ? ? ? 1.424 ? ? covale4 covale both ? A ASN 3 C ? ? ? 1_555 A GHP 4 N ? ? A ASN 3 A GHP 4 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale5 covale both ? A GHP 4 C ? ? ? 1_555 A GHP 5 N ? ? A GHP 4 A GHP 5 1_555 ? ? ? ? ? ? ? 1.349 ? ? covale6 covale none ? A GHP 4 C3 ? ? ? 1_555 A OMY 6 OCZ ? ? A GHP 4 A OMY 6 1_555 ? ? ? ? ? ? ? 1.404 ? ? covale7 covale one ? A GHP 4 O4 ? ? ? 1_555 C BGC . C1 ? ? A GHP 4 C BGC 1 1_555 ? ? ? ? ? ? ? 1.440 ? ? covale8 covale both ? A GHP 5 C ? ? ? 1_555 A OMY 6 N ? ? A GHP 5 A OMY 6 1_555 ? ? ? ? ? ? ? 1.349 ? ? covale9 covale none ? A GHP 5 C3 ? ? ? 1_555 A 3FG 7 CG1 ? ? A GHP 5 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.550 ? ? covale10 covale both ? A OMY 6 C ? ? ? 1_555 A 3FG 7 N ? ? A OMY 6 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.370 ? ? covale11 covale both ? B MLU 1 C ? ? ? 1_555 B OMZ 2 N ? ? B MLU 1 B OMZ 2 1_555 ? ? ? ? ? ? ? 1.362 ? ? covale12 covale both ? B OMZ 2 C ? ? ? 1_555 B ASN 3 N ? ? B OMZ 2 B ASN 3 1_555 ? ? ? ? ? ? ? 1.349 ? ? covale13 covale none ? B OMZ 2 OH ? ? ? 1_555 B GHP 4 C5 ? ? B OMZ 2 B GHP 4 1_555 ? ? ? ? ? ? ? 1.420 ? ? covale14 covale both ? B ASN 3 C ? ? ? 1_555 B GHP 4 N ? ? B ASN 3 B GHP 4 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale15 covale both ? B GHP 4 C ? ? ? 1_555 B GHP 5 N ? ? B GHP 4 B GHP 5 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale16 covale none ? B GHP 4 C3 ? ? ? 1_555 B OMY 6 OCZ ? ? B GHP 4 B OMY 6 1_555 ? ? ? ? ? ? ? 1.405 ? ? covale17 covale one ? B GHP 4 O4 ? ? ? 1_555 D BGC . C1 ? ? B GHP 4 D BGC 1 1_555 ? ? ? ? ? ? ? 1.437 ? ? covale18 covale both ? B GHP 5 C ? ? ? 1_555 B OMY 6 N ? ? B GHP 5 B OMY 6 1_555 ? ? ? ? ? ? ? 1.346 ? ? covale19 covale none ? B GHP 5 C3 ? ? ? 1_555 B 3FG 7 CG1 ? ? B GHP 5 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.552 ? ? covale20 covale both ? B OMY 6 C ? ? ? 1_555 B 3FG 7 N ? ? B OMY 6 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.369 ? ? covale21 covale one ? C BGC . O2 ? ? ? 1_555 C RER . C1 ? ? C BGC 1 C RER 2 1_555 ? ? ? ? ? ? ? 1.458 ? ? covale22 covale one ? D BGC . O2 ? ? ? 1_555 D RER . C1 ? ? D BGC 1 D RER 2 1_555 ? ? ? ? ? ? ? 1.464 ? ? metalc1 metalc ? ? A MLU 1 N ? ? ? 1_555 F ZN . ZN ? ? A MLU 1 B ZN 103 8_444 ? ? ? ? ? ? ? 2.149 ? ? metalc2 metalc ? ? A MLU 1 O ? ? ? 1_555 F ZN . ZN ? ? A MLU 1 B ZN 103 8_444 ? ? ? ? ? ? ? 2.187 ? ? metalc3 metalc ? ? H HOH . O ? ? ? 1_555 F ZN . ZN ? ? A HOH 209 B ZN 103 1_555 ? ? ? ? ? ? ? 2.126 ? ? metalc4 metalc ? ? B MLU 1 N ? ? ? 1_555 F ZN . ZN ? ? B MLU 1 B ZN 103 1_555 ? ? ? ? ? ? ? 2.145 ? ? metalc5 metalc ? ? B MLU 1 O ? ? ? 1_555 F ZN . ZN ? ? B MLU 1 B ZN 103 1_555 ? ? ? ? ? ? ? 2.180 ? ? metalc6 metalc ? ? F ZN . ZN ? ? ? 1_555 I HOH . O ? ? B ZN 103 B HOH 221 1_555 ? ? ? ? ? ? ? 2.132 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GHP 5 A . ? GHP 5 A OMY 6 A ? OMY 6 A 1 10.38 2 GHP 5 B . ? GHP 5 B OMY 6 B ? OMY 6 B 1 11.09 # _atom_sites.entry_id 5M2K _atom_sites.fract_transf_matrix[1][1] 0.027856 _atom_sites.fract_transf_matrix[1][2] 0.016083 _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] 0.032165 _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] 0.018001 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C CL N O ZN # 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 MLU 1 1 1 MLU MLU A . n A 1 2 OMZ 2 2 2 OMZ OMZ A . n A 1 3 ASN 3 3 3 ASN ASN A . n A 1 4 GHP 4 4 4 GHP GHP A . n A 1 5 GHP 5 5 5 GHP GHP A . n A 1 6 OMY 6 6 6 OMY OMY A . n A 1 7 3FG 7 7 7 3FG 3FG A . n B 1 1 MLU 1 1 1 MLU MLU B . n B 1 2 OMZ 2 2 2 OMZ OMZ B . n B 1 3 ASN 3 3 3 ASN ASN B . n B 1 4 GHP 4 4 4 GHP GHP B . n B 1 5 GHP 5 5 5 GHP GHP B . n B 1 6 OMY 6 6 6 OMY OMY B . n B 1 7 3FG 7 7 7 3FG 3FG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 3 EDO 1 103 1 EDO EDO A . F 4 ZN 1 103 1 ZN ZN B . G 3 EDO 1 104 2 EDO EDO B . H 5 HOH 1 201 72 HOH HOH A . H 5 HOH 2 202 48 HOH HOH A . H 5 HOH 3 203 8 HOH HOH A . H 5 HOH 4 204 9 HOH HOH A . H 5 HOH 5 205 39 HOH HOH A . H 5 HOH 6 206 16 HOH HOH A . H 5 HOH 7 207 30 HOH HOH A . H 5 HOH 8 208 12 HOH HOH A . H 5 HOH 9 209 29 HOH HOH A . H 5 HOH 10 210 13 HOH HOH A . H 5 HOH 11 211 26 HOH HOH A . H 5 HOH 12 212 4 HOH HOH A . H 5 HOH 13 213 71 HOH HOH A . H 5 HOH 14 214 69 HOH HOH A . H 5 HOH 15 215 70 HOH HOH A . H 5 HOH 16 216 75 HOH HOH A . H 5 HOH 17 217 51 HOH HOH A . H 5 HOH 18 218 35 HOH HOH A . H 5 HOH 19 219 18 HOH HOH A . H 5 HOH 20 220 36 HOH HOH A . H 5 HOH 21 221 45 HOH HOH A . H 5 HOH 22 222 31 HOH HOH A . H 5 HOH 23 223 59 HOH HOH A . H 5 HOH 24 224 47 HOH HOH A . H 5 HOH 25 225 42 HOH HOH A . H 5 HOH 26 226 50 HOH HOH A . I 5 HOH 1 201 73 HOH HOH B . I 5 HOH 2 202 15 HOH HOH B . I 5 HOH 3 203 6 HOH HOH B . I 5 HOH 4 204 64 HOH HOH B . I 5 HOH 5 205 14 HOH HOH B . I 5 HOH 6 206 1 HOH HOH B . I 5 HOH 7 207 68 HOH HOH B . I 5 HOH 8 208 25 HOH HOH B . I 5 HOH 9 209 7 HOH HOH B . I 5 HOH 10 210 19 HOH HOH B . I 5 HOH 11 211 28 HOH HOH B . I 5 HOH 12 212 5 HOH HOH B . I 5 HOH 13 213 34 HOH HOH B . I 5 HOH 14 214 67 HOH HOH B . I 5 HOH 15 215 52 HOH HOH B . I 5 HOH 16 216 61 HOH HOH B . I 5 HOH 17 217 22 HOH HOH B . I 5 HOH 18 218 56 HOH HOH B . I 5 HOH 19 219 23 HOH HOH B . I 5 HOH 20 220 63 HOH HOH B . I 5 HOH 21 221 37 HOH HOH B . I 5 HOH 22 222 74 HOH HOH B . I 5 HOH 23 223 60 HOH HOH B . I 5 HOH 24 224 65 HOH HOH B . I 5 HOH 25 225 54 HOH HOH B . I 5 HOH 26 226 55 HOH HOH B . I 5 HOH 27 227 17 HOH HOH B . I 5 HOH 28 228 27 HOH HOH B . I 5 HOH 29 229 38 HOH HOH B . I 5 HOH 30 230 21 HOH HOH B . I 5 HOH 31 231 46 HOH HOH B . I 5 HOH 32 232 57 HOH HOH B . I 5 HOH 33 233 62 HOH HOH B . I 5 HOH 34 234 24 HOH HOH B . I 5 HOH 35 235 66 HOH HOH B . I 5 HOH 36 236 53 HOH HOH B . I 5 HOH 37 237 58 HOH HOH B . # _pdbx_molecule_features.prd_id PRD_000204 _pdbx_molecule_features.name VANCOMYCIN _pdbx_molecule_features.type Glycopeptide _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000204 A 1 PRD_000204 C # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA monomeric 1 2 author_and_software_defined_assembly PISA monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C,E,H 2 1 B,D,F,G,I # _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_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 201 ? H HOH . 2 1 A HOH 221 ? H HOH . 3 1 A HOH 225 ? H HOH . 4 1 B HOH 201 ? I HOH . 5 1 B HOH 222 ? I HOH . 6 1 B HOH 236 ? I HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N ? A MLU 1 ? A MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? A MLU 1 ? A MLU 1 ? 1_555 80.2 ? 2 N ? A MLU 1 ? A MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? H HOH . ? A HOH 209 ? 1_555 135.5 ? 3 O ? A MLU 1 ? A MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? H HOH . ? A HOH 209 ? 1_555 58.7 ? 4 N ? A MLU 1 ? A MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 N ? B MLU 1 ? B MLU 1 ? 1_555 139.8 ? 5 O ? A MLU 1 ? A MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 N ? B MLU 1 ? B MLU 1 ? 1_555 65.3 ? 6 O ? H HOH . ? A HOH 209 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 N ? B MLU 1 ? B MLU 1 ? 1_555 7.3 ? 7 N ? A MLU 1 ? A MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? B MLU 1 ? B MLU 1 ? 1_555 141.2 ? 8 O ? A MLU 1 ? A MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? B MLU 1 ? B MLU 1 ? 1_555 65.2 ? 9 O ? H HOH . ? A HOH 209 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? B MLU 1 ? B MLU 1 ? 1_555 6.5 ? 10 N ? B MLU 1 ? B MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? B MLU 1 ? B MLU 1 ? 1_555 2.9 ? 11 N ? A MLU 1 ? A MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? I HOH . ? B HOH 221 ? 1_555 132.0 ? 12 O ? A MLU 1 ? A MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? I HOH . ? B HOH 221 ? 1_555 58.8 ? 13 O ? H HOH . ? A HOH 209 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? I HOH . ? B HOH 221 ? 1_555 7.1 ? 14 N ? B MLU 1 ? B MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? I HOH . ? B HOH 221 ? 1_555 7.8 ? 15 O ? B MLU 1 ? B MLU 1 ? 1_555 ZN ? F ZN . ? B ZN 103 ? 8_444 O ? I HOH . ? B HOH 221 ? 1_555 9.6 ? # 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 2017-07-19 2 'Structure model' 2 0 2018-06-13 3 'Structure model' 3 0 2019-04-24 4 'Structure model' 3 1 2019-07-10 5 'Structure model' 4 0 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 5 'Structure model' repository Remediation 'Carbohydrate remediation' ? # 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' 'Atomic model' 2 2 'Structure model' 'Data collection' 3 2 'Structure model' 'Database references' 4 2 'Structure model' 'Structure summary' 5 3 'Structure model' Advisory 6 3 'Structure model' 'Data collection' 7 3 'Structure model' 'Derived calculations' 8 3 'Structure model' 'Polymer sequence' 9 4 'Structure model' 'Data collection' 10 5 'Structure model' 'Atomic model' 11 5 'Structure model' 'Data collection' 12 5 'Structure model' 'Derived calculations' 13 5 'Structure model' 'Structure summary' # 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' atom_site 2 2 'Structure model' pdbx_entry_details 3 2 'Structure model' pdbx_molecule_features 4 2 'Structure model' struct_ref 5 3 'Structure model' diffrn_source 6 3 'Structure model' entity_poly 7 3 'Structure model' pdbx_seq_map_depositor_info 8 3 'Structure model' pdbx_struct_special_symmetry 9 3 'Structure model' pdbx_validate_close_contact 10 3 'Structure model' pdbx_validate_symm_contact 11 4 'Structure model' diffrn_source 12 5 'Structure model' atom_site 13 5 'Structure model' atom_site_anisotrop 14 5 'Structure model' chem_comp 15 5 'Structure model' entity 16 5 'Structure model' pdbx_branch_scheme 17 5 'Structure model' pdbx_chem_comp_identifier 18 5 'Structure model' pdbx_entity_branch 19 5 'Structure model' pdbx_entity_branch_descriptor 20 5 'Structure model' pdbx_entity_branch_link 21 5 'Structure model' pdbx_entity_branch_list 22 5 'Structure model' pdbx_entity_nonpoly 23 5 'Structure model' pdbx_molecule 24 5 'Structure model' pdbx_nonpoly_scheme 25 5 'Structure model' pdbx_struct_assembly_gen 26 5 'Structure model' pdbx_struct_conn_angle 27 5 'Structure model' pdbx_struct_special_symmetry 28 5 'Structure model' struct_asym 29 5 'Structure model' struct_conn 30 5 'Structure model' struct_site 31 5 'Structure model' struct_site_gen # 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' '_atom_site.occupancy' 2 2 'Structure model' '_struct_ref.db_name' 3 2 'Structure model' '_struct_ref.pdbx_db_accession' 4 3 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 5 3 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 6 3 'Structure model' '_pdbx_seq_map_depositor_info.one_letter_code' 7 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 8 5 'Structure model' '_atom_site.B_iso_or_equiv' 9 5 'Structure model' '_atom_site.Cartn_x' 10 5 'Structure model' '_atom_site.Cartn_y' 11 5 'Structure model' '_atom_site.Cartn_z' 12 5 'Structure model' '_atom_site.auth_asym_id' 13 5 'Structure model' '_atom_site.auth_atom_id' 14 5 'Structure model' '_atom_site.auth_comp_id' 15 5 'Structure model' '_atom_site.auth_seq_id' 16 5 'Structure model' '_atom_site.label_asym_id' 17 5 'Structure model' '_atom_site.label_atom_id' 18 5 'Structure model' '_atom_site.label_comp_id' 19 5 'Structure model' '_atom_site.label_entity_id' 20 5 'Structure model' '_atom_site.type_symbol' 21 5 'Structure model' '_atom_site_anisotrop.U[1][1]' 22 5 'Structure model' '_atom_site_anisotrop.U[1][2]' 23 5 'Structure model' '_atom_site_anisotrop.U[1][3]' 24 5 'Structure model' '_atom_site_anisotrop.U[2][2]' 25 5 'Structure model' '_atom_site_anisotrop.U[2][3]' 26 5 'Structure model' '_atom_site_anisotrop.U[3][3]' 27 5 'Structure model' '_atom_site_anisotrop.pdbx_auth_asym_id' 28 5 'Structure model' '_atom_site_anisotrop.pdbx_auth_atom_id' 29 5 'Structure model' '_atom_site_anisotrop.pdbx_auth_comp_id' 30 5 'Structure model' '_atom_site_anisotrop.pdbx_auth_seq_id' 31 5 'Structure model' '_atom_site_anisotrop.pdbx_label_asym_id' 32 5 'Structure model' '_atom_site_anisotrop.pdbx_label_atom_id' 33 5 'Structure model' '_atom_site_anisotrop.pdbx_label_comp_id' 34 5 'Structure model' '_atom_site_anisotrop.type_symbol' 35 5 'Structure model' '_chem_comp.name' 36 5 'Structure model' '_chem_comp.type' 37 5 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 38 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 39 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 40 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 41 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 42 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 43 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 44 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 45 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 46 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_symmetry' 47 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 48 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 49 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 50 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 51 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 52 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 53 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 54 5 'Structure model' '_pdbx_struct_conn_angle.value' 55 5 'Structure model' '_pdbx_struct_special_symmetry.label_asym_id' 56 5 'Structure model' '_struct_conn.conn_type_id' 57 5 'Structure model' '_struct_conn.id' 58 5 'Structure model' '_struct_conn.pdbx_dist_value' 59 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 60 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 61 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 62 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 63 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 64 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 65 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 66 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 67 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 68 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 69 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 70 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 71 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 72 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 73 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 74 5 'Structure model' '_struct_conn.ptnr2_symmetry' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0135 1 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.20 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? SCALA ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _pdbx_entry_details.entry_id 5M2K _pdbx_entry_details.compound_details ;VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE AND VANCOSAMINE. HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOUGHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # 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 HOH 217 ? ? O A HOH 219 ? ? 1.37 2 1 O A HOH 224 ? ? O B HOH 231 ? ? 1.94 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O B HOH 215 ? ? 1_555 O B HOH 227 ? ? 6_445 1.35 2 1 O A HOH 202 ? ? 1_555 O A HOH 212 ? ? 3_555 1.78 3 1 OXT A 3FG 7 ? ? 1_555 O A HOH 202 ? ? 2_555 1.90 4 1 CN A MLU 1 ? ? 1_555 O A HOH 216 ? ? 9_444 2.16 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CA _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 ASN _pdbx_validate_rmsd_bond.auth_seq_id_1 3 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 CB _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 ASN _pdbx_validate_rmsd_bond.auth_seq_id_2 3 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.684 _pdbx_validate_rmsd_bond.bond_target_value 1.527 _pdbx_validate_rmsd_bond.bond_deviation 0.157 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.026 _pdbx_validate_rmsd_bond.linker_flag N # 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 ASN A 3 ? ? -167.42 -140.91 2 1 ASN B 3 ? ? -169.08 -142.05 # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 226 ? 6.74 . 2 1 O ? B HOH 237 ? 6.55 . # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero C 2 BGC 1 C BGC 1 A BGC 8 n C 2 RER 2 C RER 2 A RER 9 n D 2 BGC 1 D BGC 1 B BGC 8 n D 2 RER 2 D RER 2 B RER 9 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier BGC 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpb BGC 'COMMON NAME' GMML 1.0 b-D-glucopyranose BGC 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-Glcp BGC 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Glc # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 2 'WURCS=2.0/2,2,1/[a2122h-1b_1-5][ad621m-1a_1-5_3*C_3*N]/1-2/a2-b1' WURCS PDB2Glycan 1.1.0 2 2 '[][D-1-deoxy-Glcp]{[(2+1)][a-L-2-deoxy-Fucp3N]{}}' LINUCS PDB-CARE ? # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.comp_id_1 RER _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.details ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 2 BGC 1 n 2 RER 2 n # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 1,2-ETHANEDIOL EDO 4 'ZINC ION' ZN 5 water HOH #