data_1C0R # _entry.id 1C0R # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _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 1C0R pdb_00001c0r 10.2210/pdb1c0r/pdb RCSB RCSB001237 ? ? WWPDB D_1000001237 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1AA5 unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN' PDB 1C0Q unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH 2-ACETOXY-D-PROPANOIC ACID' PDB 1FVM unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH DI-ACETYL-LYS-D-ALA-D-ALA' PDB 1GAC unspecified 'SOLUTION STRUCTURE OF A82846B COMPLEXED WITH ITS CELL WALL PENTAPEPTIDE FRAGMENT' PDB 1GHG unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON' PDB 1PN3 unspecified 'CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXD WITH TDP AND DESVANCOSAMINYL VANCOMYCIN' PDB 1PNV unspecified 'CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXED WITH TDP AND VANCOMYCIN' PDB 1QD8 unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH N-ACETYL GLYCIN' PDB 1RRV unspecified 'CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEXED WITH TDP AND DESVANCOSAMINYL VANCOMYCIN.' PDB 1SHO unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN' # _pdbx_database_status.entry_id 1C0R _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 1999-07-20 _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Loll, P.J.' 1 'Kaplan, J.' 2 'Selinsky, B.' 3 'Axelsen, P.H.' 4 # _citation.id primary _citation.title 'Vancomycin Binding to Low-Affinity Ligands: Delineating a Minimum Set of Interactions Necessary for High-Affinity Binding.' _citation.journal_abbrev J.Med.Chem. _citation.journal_volume 42 _citation.page_first 4714 _citation.page_last ? _citation.year 1999 _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 10579833 _citation.pdbx_database_id_DOI 10.1021/JM990361T # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Loll, P.J.' 1 ? primary 'Kaplan, J.' 2 ? primary 'Selinsky, B.S.' 3 ? primary 'Axelsen, P.H.' 4 ? # _cell.entry_id 1C0R _cell.length_a 28.440 _cell.length_b 28.440 _cell.length_c 66.040 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1C0R _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # 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 man VANCOMYCIN 1149.977 2 ? ? ? ? 2 branched man 'vancosamine-(1-2)-beta-D-glucopyranose' 323.340 2 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 3 ? ? ? ? 4 non-polymer syn 'LACTIC ACID' 90.078 1 ? ? ? ? 5 water nat water 18.015 45 ? ? ? ? # _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_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'AMYCOLATOPSIS ORIENTALIS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 31958 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name ? _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ? _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name NOR _struct_ref.db_code NOR00681 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession NOR00681 _struct_ref.pdbx_db_isoform ? # 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 1C0R A 1 ? 7 ? NOR00681 1 ? 7 ? 1 7 2 1 1C0R B 1 ? 7 ? NOR00681 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 'beta-D-glucose; D-glucose; glucose' 'C6 H12 O6' 180.156 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 GHP 'D-peptide linking' . '(2R)-amino(4-hydroxyphenyl)ethanoic acid' ? 'C8 H9 N O3' 167.162 HOH non-polymer . WATER ? 'H2 O' 18.015 LAC non-polymer . 'LACTIC ACID' ? 'C3 H6 O3' 90.078 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 '(1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose' 'C7 H15 N O3' 161.199 # _exptl.entry_id 1C0R _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.90 _exptl_crystal.density_percent_sol 57.63 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'SODIUM CHLORIDE, LACTIC ACID, PH 4.6, VAPOR DIFFUSION/HANGING DROP, TEMPERATURE 291K' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type CUSTOM-MADE _diffrn_detector.pdbx_collection_date 1996-09-20 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.918 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'CHESS BEAMLINE A1' _diffrn_source.pdbx_synchrotron_site CHESS _diffrn_source.pdbx_synchrotron_beamline A1 _diffrn_source.pdbx_wavelength 0.918 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 1C0R _reflns.observed_criterion_sigma_I 2.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 1.000 _reflns.number_obs 13896 _reflns.number_all ? _reflns.percent_possible_obs 97.0 _reflns.pdbx_Rmerge_I_obs 0.05200 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 29.8000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 16.400 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.00 _reflns_shell.d_res_low 1.04 _reflns_shell.percent_possible_all 54.0 _reflns_shell.Rmerge_I_obs 0.06500 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 1.90 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 1C0R _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 14301 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.00 _refine.ls_d_res_high 1.00 _refine.ls_percent_reflns_obs 97.0 _refine.ls_R_factor_obs 0.114 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.142 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 934 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;REFINEMENT WAS CARRIED OUT AGAINST F -SQUARED USING SHELXL-93. MOLECULAR GEOMETRY AND ATOMIC DISPLACEMENT PARAMETERS WERE RESTRAINED THROUGHOUT. INDEPENDENT VANCOMYCIN MONOMERS WERE RESTRAINED TO HAVE SIMILAR 1-2 AND 1-3 DISTANCES; RESTRAINTS WERE ALSO IMPOSED TO LIMIT DEVIATIONS FROM PLANARITY IN RINGS AND SP2 SYSTEMS. ALONG-BOND COMPONENTS OF ANISOTROPIC DISPLACEMENT PARAMETERS WERE SUBJECTED TO RESTRAINTS. SOLVENT WATER ATOMS WERE RESTRAINED TO BE APPROXIMATELY ISOTROPIC AND WERE MADE SUBJECT TO ANTI-BUMPING RESTRAINTS. CONJUGATE GRADIENT REFINEMENT WAS USED THROUGHOUT, EXCEPT AT THE LAST STAGES, WHEN BLOCKED LEAST SQUARES WAS USED. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'ENGH & HUBER' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 160 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 51 _refine_hist.number_atoms_solvent 45 _refine_hist.number_atoms_total 256 _refine_hist.d_res_high 1.00 _refine_hist.d_res_low 20.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.019 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 1C0R _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.114 _pdbx_refine.free_R_factor_no_cutoff 0.142 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff 934 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? # _struct.entry_id 1C0R _struct.title 'COMPLEX OF VANCOMYCIN WITH D-LACTIC ACID' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1C0R _struct_keywords.pdbx_keywords ANTIBIOTIC _struct_keywords.text 'ANTIBIOTIC, GLYCOPEPTIDE 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 3 ? G N N 3 ? H N N 4 ? I N N 5 ? J N N 5 ? # _struct_biol.id 1 # 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 ? ? ? ? ? ? ? 1.364 ? ? covale2 covale both ? A OMZ 2 C ? ? ? 1_555 A ASN 3 N ? ? A OMZ 2 A ASN 3 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale3 covale none ? A OMZ 2 OH ? ? ? 1_555 A GHP 4 C5 ? ? A OMZ 2 A GHP 4 1_555 ? ? ? ? ? ? ? 1.400 ? ? covale4 covale both ? A ASN 3 C ? ? ? 1_555 A GHP 4 N ? ? A ASN 3 A GHP 4 1_555 ? ? ? ? ? ? ? 1.337 ? ? 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 ? ? ? ? ? ? ? 1.383 ? ? covale7 covale one ? A GHP 4 O4 ? ? ? 1_555 C BGC . C1 ? ? A GHP 4 C BGC 1 1_555 ? ? ? ? ? ? ? 1.427 ? ? covale8 covale both ? A GHP 5 C ? ? ? 1_555 A OMY 6 N ? ? A GHP 5 A OMY 6 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale9 covale one ? A GHP 5 C3 ? ? ? 1_555 A 3FG 7 CG1 ? ? A GHP 5 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.470 ? ? covale10 covale both ? A OMY 6 C ? ? ? 1_555 A 3FG 7 N ? ? A OMY 6 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale11 covale both ? B MLU 1 C ? ? ? 1_555 B OMZ 2 N ? ? B MLU 1 B OMZ 2 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale12 covale both ? B OMZ 2 C ? ? ? 1_555 B ASN 3 N ? ? B OMZ 2 B ASN 3 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale13 covale none ? B OMZ 2 OH ? ? ? 1_555 B GHP 4 C5 ? ? B OMZ 2 B GHP 4 1_555 ? ? ? ? ? ? ? 1.392 ? ? 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 ? ? ? ? ? ? ? 1.338 ? ? covale16 covale none ? B GHP 4 C3 ? ? ? 1_555 B OMY 6 OCZ ? ? B GHP 4 B OMY 6 1_555 ? ? ? ? ? ? ? 1.369 ? ? covale17 covale one ? B GHP 4 O4 B ? ? 1_555 D BGC . C1 B ? B GHP 4 D BGC 1 1_555 ? ? ? ? ? ? ? 1.432 ? ? covale18 covale one ? B GHP 4 O4 A ? ? 1_555 D BGC . C1 A ? B GHP 4 D BGC 1 1_555 ? ? ? ? ? ? ? 1.434 ? ? covale19 covale both ? B GHP 5 C ? ? ? 1_555 B OMY 6 N ? ? B GHP 5 B OMY 6 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale20 covale one ? B GHP 5 C3 ? ? ? 1_555 B 3FG 7 CG1 ? ? B GHP 5 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.482 ? ? covale21 covale both ? B OMY 6 C ? ? ? 1_555 B 3FG 7 N ? ? B OMY 6 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale22 covale both ? C BGC . O2 ? ? ? 1_555 C RER . C1 ? ? C BGC 1 C RER 2 1_555 ? ? ? ? ? ? ? 1.425 ? ? covale23 covale both ? D BGC . O2 B ? ? 1_555 D RER . C1 ? ? D BGC 1 D RER 2 1_555 ? ? ? ? ? ? ? 1.113 ? ? covale24 covale both ? D BGC . O2 A ? ? 1_555 D RER . C1 ? ? D BGC 1 D RER 2 1_555 ? ? ? ? ? ? ? 1.477 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 6.16 2 GHP 5 B . ? GHP 5 B OMY 6 B ? OMY 6 B 1 19.74 # _database_PDB_matrix.entry_id 1C0R _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1C0R _atom_sites.fract_transf_matrix[1][1] 0.035162 _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] 0.035162 _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] 0.015142 _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 CL 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 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 CL 1 20 20 CL CL A . F 3 CL 1 21 21 CL CL A . G 3 CL 1 22 22 CL CL B . H 4 LAC 1 23 23 LAC LAC B . I 5 HOH 1 2001 2001 HOH HOH A . I 5 HOH 2 2002 2002 HOH HOH A . I 5 HOH 3 2003 2003 HOH HOH A . I 5 HOH 4 2004 2004 HOH HOH A . I 5 HOH 5 2005 2005 HOH HOH A . I 5 HOH 6 2006 2006 HOH HOH A . I 5 HOH 7 2007 2007 HOH HOH A . I 5 HOH 8 2008 2008 HOH HOH A . I 5 HOH 9 2009 2009 HOH HOH A . I 5 HOH 10 2010 2010 HOH HOH A . I 5 HOH 11 2011 2011 HOH HOH A . I 5 HOH 12 2012 2012 HOH HOH A . I 5 HOH 13 2013 2013 HOH HOH A . I 5 HOH 14 2014 2014 HOH HOH A . I 5 HOH 15 2015 2015 HOH HOH A . I 5 HOH 16 2016 2016 HOH HOH A . I 5 HOH 17 2017 2017 HOH HOH A . I 5 HOH 18 2018 2018 HOH HOH A . I 5 HOH 19 2019 2019 HOH HOH A . I 5 HOH 20 2020 2020 HOH HOH A . I 5 HOH 21 2021 2021 HOH HOH A . I 5 HOH 22 2022 2022 HOH HOH A . I 5 HOH 23 2023 2023 HOH HOH A . I 5 HOH 24 2024 2024 HOH HOH A . I 5 HOH 25 2025 2025 HOH HOH A . J 5 HOH 1 2001 2001 HOH HOH B . J 5 HOH 2 2002 2002 HOH HOH B . J 5 HOH 3 2003 2003 HOH HOH B . J 5 HOH 4 2004 2004 HOH HOH B . J 5 HOH 5 2005 2005 HOH HOH B . J 5 HOH 6 2006 2006 HOH HOH B . J 5 HOH 7 2007 2007 HOH HOH B . J 5 HOH 8 2008 2008 HOH HOH B . J 5 HOH 9 2009 2009 HOH HOH B . J 5 HOH 10 2010 2010 HOH HOH B . J 5 HOH 11 2011 2011 HOH HOH B . J 5 HOH 12 2012 2012 HOH HOH B . J 5 HOH 13 2013 2013 HOH HOH B . J 5 HOH 14 2014 2014 HOH HOH B . J 5 HOH 15 2015 2015 HOH HOH B . J 5 HOH 16 2016 2016 HOH HOH B . J 5 HOH 17 2017 2017 HOH HOH B . J 5 HOH 18 2018 2018 HOH HOH B . J 5 HOH 19 2019 2019 HOH HOH B . J 5 HOH 20 2020 2020 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 2 PRD_000204 B 2 PRD_000204 D # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,C,E,F,I 1 3,4 B,D,G,H,J # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 4170 ? 1 MORE -68.4 ? 1 'SSA (A^2)' 3680 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'crystal symmetry operation' 4_455 y-1/2,-x+1/2,z+1/4 0.0000000000 1.0000000000 0.0000000000 -14.2200000000 -1.0000000000 0.0000000000 0.0000000000 14.2200000000 0.0000000000 0.0000000000 1.0000000000 16.5100000000 2 'crystal symmetry operation' 6_455 x-1/2,-y+1/2,-z+1/4 1.0000000000 0.0000000000 0.0000000000 -14.2200000000 0.0000000000 -1.0000000000 0.0000000000 14.2200000000 0.0000000000 0.0000000000 -1.0000000000 16.5100000000 3 'crystal symmetry operation' 8_555 -y,-x,-z+1/2 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 33.0200000000 4 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 2012 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id I _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 1999-07-30 2 'Structure model' 1 1 2011-06-14 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-07-27 5 'Structure model' 1 4 2012-12-12 6 'Structure model' 2 0 2020-07-29 7 'Structure model' 3 0 2023-11-15 # 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 6 '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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Non-polymer description' 7 4 'Structure model' 'Structure summary' 8 5 'Structure model' Other 9 6 'Structure model' Advisory 10 6 'Structure model' 'Atomic model' 11 6 'Structure model' 'Data collection' 12 6 'Structure model' 'Derived calculations' 13 6 'Structure model' 'Polymer sequence' 14 6 'Structure model' 'Refinement description' 15 6 'Structure model' 'Structure summary' 16 7 'Structure model' 'Atomic model' 17 7 'Structure model' 'Data collection' 18 7 'Structure model' 'Database references' 19 7 'Structure model' 'Derived calculations' 20 7 '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 6 'Structure model' atom_site 2 6 'Structure model' chem_comp 3 6 'Structure model' entity 4 6 'Structure model' entity_poly 5 6 'Structure model' pdbx_branch_scheme 6 6 'Structure model' pdbx_chem_comp_identifier 7 6 'Structure model' pdbx_entity_branch 8 6 'Structure model' pdbx_entity_branch_descriptor 9 6 'Structure model' pdbx_entity_branch_link 10 6 'Structure model' pdbx_entity_branch_list 11 6 'Structure model' pdbx_entity_nonpoly 12 6 'Structure model' pdbx_molecule 13 6 'Structure model' pdbx_nonpoly_scheme 14 6 'Structure model' pdbx_struct_assembly 15 6 'Structure model' pdbx_struct_assembly_gen 16 6 'Structure model' pdbx_struct_special_symmetry 17 6 'Structure model' pdbx_validate_close_contact 18 6 'Structure model' software 19 6 'Structure model' struct_asym 20 6 'Structure model' struct_conn 21 6 'Structure model' struct_site 22 6 'Structure model' struct_site_gen 23 7 'Structure model' atom_site 24 7 'Structure model' chem_comp 25 7 'Structure model' chem_comp_atom 26 7 'Structure model' chem_comp_bond 27 7 'Structure model' database_2 28 7 'Structure model' struct_conn # 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 6 'Structure model' '_atom_site.B_iso_or_equiv' 2 6 'Structure model' '_atom_site.Cartn_x' 3 6 'Structure model' '_atom_site.Cartn_y' 4 6 'Structure model' '_atom_site.Cartn_z' 5 6 'Structure model' '_atom_site.auth_asym_id' 6 6 'Structure model' '_atom_site.auth_atom_id' 7 6 'Structure model' '_atom_site.auth_comp_id' 8 6 'Structure model' '_atom_site.auth_seq_id' 9 6 'Structure model' '_atom_site.label_alt_id' 10 6 'Structure model' '_atom_site.label_asym_id' 11 6 'Structure model' '_atom_site.label_atom_id' 12 6 'Structure model' '_atom_site.label_comp_id' 13 6 'Structure model' '_atom_site.label_entity_id' 14 6 'Structure model' '_atom_site.occupancy' 15 6 'Structure model' '_atom_site.type_symbol' 16 6 'Structure model' '_chem_comp.name' 17 6 'Structure model' '_chem_comp.type' 18 6 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 19 6 'Structure model' '_pdbx_struct_assembly.method_details' 20 6 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 21 6 'Structure model' '_pdbx_struct_special_symmetry.label_asym_id' 22 6 'Structure model' '_pdbx_validate_close_contact.auth_asym_id_1' 23 6 'Structure model' '_pdbx_validate_close_contact.auth_asym_id_2' 24 6 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_1' 25 6 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_2' 26 6 'Structure model' '_struct_conn.pdbx_dist_value' 27 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 28 6 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 29 6 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 30 6 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 31 6 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 32 6 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 33 6 'Structure model' '_struct_conn.ptnr1_label_asym_id' 34 6 'Structure model' '_struct_conn.ptnr1_label_atom_id' 35 6 'Structure model' '_struct_conn.ptnr1_label_comp_id' 36 6 'Structure model' '_struct_conn.ptnr1_label_seq_id' 37 6 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 38 6 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 39 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 40 6 'Structure model' '_struct_conn.ptnr2_label_asym_id' 41 6 'Structure model' '_struct_conn.ptnr2_label_atom_id' 42 6 'Structure model' '_struct_conn.ptnr2_label_comp_id' 43 6 'Structure model' '_struct_conn.ptnr2_label_seq_id' 44 7 'Structure model' '_atom_site.auth_atom_id' 45 7 'Structure model' '_atom_site.label_atom_id' 46 7 'Structure model' '_chem_comp.pdbx_synonyms' 47 7 'Structure model' '_database_2.pdbx_DOI' 48 7 'Structure model' '_database_2.pdbx_database_accession' 49 7 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL refinement . ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 # _pdbx_entry_details.entry_id 1C0R _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 O2 D BGC 1 ? B O5 D RER 2 ? ? 2.02 2 1 C2 D BGC 1 ? B C1 D RER 2 ? ? 2.15 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ASN _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 3 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -100.24 _pdbx_validate_torsion.psi -68.57 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 3FG N N N N 1 3FG OD1 O N N 2 3FG CD1 C Y N 3 3FG CG1 C Y N 4 3FG CZ C Y N 5 3FG CD2 C Y N 6 3FG OD2 O N N 7 3FG CG2 C Y N 8 3FG CB C Y N 9 3FG CA C N S 10 3FG C C N N 11 3FG O O N N 12 3FG OXT O N N 13 3FG H H N N 14 3FG H2 H N N 15 3FG HA H N N 16 3FG HD1 H N N 17 3FG HG1 H N N 18 3FG HZ H N N 19 3FG HD2 H N N 20 3FG HG2 H N N 21 3FG HXT H N N 22 ASN N N N N 23 ASN CA C N S 24 ASN C C N N 25 ASN O O N N 26 ASN CB C N N 27 ASN CG C N N 28 ASN OD1 O N N 29 ASN ND2 N N N 30 ASN OXT O N N 31 ASN H H N N 32 ASN H2 H N N 33 ASN HA H N N 34 ASN HB2 H N N 35 ASN HB3 H N N 36 ASN HD21 H N N 37 ASN HD22 H N N 38 ASN HXT H N N 39 BGC C2 C N R 40 BGC C3 C N S 41 BGC C4 C N S 42 BGC C5 C N R 43 BGC C6 C N N 44 BGC C1 C N R 45 BGC O1 O N N 46 BGC O2 O N N 47 BGC O3 O N N 48 BGC O4 O N N 49 BGC O5 O N N 50 BGC O6 O N N 51 BGC H2 H N N 52 BGC H3 H N N 53 BGC H4 H N N 54 BGC H5 H N N 55 BGC H61 H N N 56 BGC H62 H N N 57 BGC H1 H N N 58 BGC HO1 H N N 59 BGC HO2 H N N 60 BGC HO3 H N N 61 BGC HO4 H N N 62 BGC HO6 H N N 63 CL CL CL N N 64 GHP N N N N 65 GHP CA C N R 66 GHP C C N N 67 GHP O O N N 68 GHP OXT O N N 69 GHP C1 C Y N 70 GHP C2 C Y N 71 GHP C3 C Y N 72 GHP C4 C Y N 73 GHP O4 O N N 74 GHP C5 C Y N 75 GHP C6 C Y N 76 GHP H H N N 77 GHP H2 H N N 78 GHP HA H N N 79 GHP HXT H N N 80 GHP HC2 H N N 81 GHP H3 H N N 82 GHP HO4 H N N 83 GHP H5 H N N 84 GHP H6 H N N 85 HOH O O N N 86 HOH H1 H N N 87 HOH H2 H N N 88 LAC C C N N 89 LAC CA C N R 90 LAC CB C N N 91 LAC O O N N 92 LAC OHN O N N 93 LAC OXT O N N 94 LAC HA H N N 95 LAC HB1 H N N 96 LAC HB2 H N N 97 LAC HB3 H N N 98 LAC H H N N 99 LAC HXT H N N 100 MLU N N N N 101 MLU CN C N N 102 MLU CA C N R 103 MLU C C N N 104 MLU O O N N 105 MLU CB C N N 106 MLU CG C N N 107 MLU CD1 C N N 108 MLU CD2 C N N 109 MLU OXT O N N 110 MLU H H N N 111 MLU HCN1 H N N 112 MLU HCN2 H N N 113 MLU HCN3 H N N 114 MLU HA H N N 115 MLU HB2 H N N 116 MLU HB3 H N N 117 MLU HXT H N N 118 MLU HG H N N 119 MLU HD11 H N N 120 MLU HD12 H N N 121 MLU HD13 H N N 122 MLU HD21 H N N 123 MLU HD22 H N N 124 MLU HD23 H N N 125 OMY N N N N 126 OMY CA C N S 127 OMY OCZ O N N 128 OMY CE2 C Y N 129 OMY CE1 C Y N 130 OMY CZ C Y N 131 OMY CG C Y N 132 OMY CD2 C Y N 133 OMY CD1 C Y N 134 OMY CB C N R 135 OMY CL CL N N 136 OMY O O N N 137 OMY C C N N 138 OMY ODE O N N 139 OMY OXT O N N 140 OMY H H N N 141 OMY H2 H N N 142 OMY HA H N N 143 OMY HCZ H N N 144 OMY HE2 H N N 145 OMY HD2 H N N 146 OMY HD1 H N N 147 OMY HB H N N 148 OMY HXT H N N 149 OMY HDE H N N 150 OMZ N N N N 151 OMZ CA C N R 152 OMZ C C N N 153 OMZ O O N N 154 OMZ OXT O N N 155 OMZ CB C N R 156 OMZ OC O N N 157 OMZ CG C Y N 158 OMZ CD1 C Y N 159 OMZ CD2 C Y N 160 OMZ CE1 C Y N 161 OMZ CL CL N N 162 OMZ CE2 C Y N 163 OMZ CZ C Y N 164 OMZ OH O N N 165 OMZ H H N N 166 OMZ H2 H N N 167 OMZ HA H N N 168 OMZ HB H N N 169 OMZ HXT H N N 170 OMZ HC H N N 171 OMZ HD1 H N N 172 OMZ HD2 H N N 173 OMZ HE2 H N N 174 OMZ HH H N N 175 RER C1 C N R 176 RER C2 C N N 177 RER C3 C N S 178 RER N3 N N N 179 RER C3A C N N 180 RER C4 C N S 181 RER O4 O N N 182 RER C5 C N S 183 RER O5 O N N 184 RER C5A C N N 185 RER O1 O N N 186 RER H1 H N N 187 RER H21C H N N 188 RER H22C H N N 189 RER HO1 H N N 190 RER H31N H N N 191 RER H32N H N N 192 RER H3A1 H N N 193 RER H3A2 H N N 194 RER H3A3 H N N 195 RER H4 H N N 196 RER HO4 H N N 197 RER H5 H N N 198 RER H5A1 H N N 199 RER H5A2 H N N 200 RER H5A3 H N N 201 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 3FG N CA sing N N 1 3FG OD1 CD1 sing N N 2 3FG CD1 CG1 sing Y N 3 3FG CD1 CZ doub Y N 4 3FG CG1 CB doub Y N 5 3FG CZ CD2 sing Y N 6 3FG CD2 OD2 sing N N 7 3FG CD2 CG2 doub Y N 8 3FG CG2 CB sing Y N 9 3FG CB CA sing N N 10 3FG CA C sing N N 11 3FG C O doub N N 12 3FG C OXT sing N N 13 3FG N H sing N N 14 3FG N H2 sing N N 15 3FG CA HA sing N N 16 3FG OD1 HD1 sing N N 17 3FG CG1 HG1 sing N N 18 3FG CZ HZ sing N N 19 3FG OD2 HD2 sing N N 20 3FG CG2 HG2 sing N N 21 3FG OXT HXT sing N N 22 ASN N CA sing N N 23 ASN N H sing N N 24 ASN N H2 sing N N 25 ASN CA C sing N N 26 ASN CA CB sing N N 27 ASN CA HA sing N N 28 ASN C O doub N N 29 ASN C OXT sing N N 30 ASN CB CG sing N N 31 ASN CB HB2 sing N N 32 ASN CB HB3 sing N N 33 ASN CG OD1 doub N N 34 ASN CG ND2 sing N N 35 ASN ND2 HD21 sing N N 36 ASN ND2 HD22 sing N N 37 ASN OXT HXT sing N N 38 BGC C2 C3 sing N N 39 BGC C2 C1 sing N N 40 BGC C2 O2 sing N N 41 BGC C2 H2 sing N N 42 BGC C3 C4 sing N N 43 BGC C3 O3 sing N N 44 BGC C3 H3 sing N N 45 BGC C4 C5 sing N N 46 BGC C4 O4 sing N N 47 BGC C4 H4 sing N N 48 BGC C5 C6 sing N N 49 BGC C5 O5 sing N N 50 BGC C5 H5 sing N N 51 BGC C6 O6 sing N N 52 BGC C6 H61 sing N N 53 BGC C6 H62 sing N N 54 BGC C1 O1 sing N N 55 BGC C1 O5 sing N N 56 BGC C1 H1 sing N N 57 BGC O1 HO1 sing N N 58 BGC O2 HO2 sing N N 59 BGC O3 HO3 sing N N 60 BGC O4 HO4 sing N N 61 BGC O6 HO6 sing N N 62 GHP N CA sing N N 63 GHP N H sing N N 64 GHP N H2 sing N N 65 GHP CA C sing N N 66 GHP CA C1 sing N N 67 GHP CA HA sing N N 68 GHP C O doub N N 69 GHP C OXT sing N N 70 GHP OXT HXT sing N N 71 GHP C1 C2 doub Y N 72 GHP C1 C6 sing Y N 73 GHP C2 C3 sing Y N 74 GHP C2 HC2 sing N N 75 GHP C3 C4 doub Y N 76 GHP C3 H3 sing N N 77 GHP C4 O4 sing N N 78 GHP C4 C5 sing Y N 79 GHP O4 HO4 sing N N 80 GHP C5 C6 doub Y N 81 GHP C5 H5 sing N N 82 GHP C6 H6 sing N N 83 HOH O H1 sing N N 84 HOH O H2 sing N N 85 LAC C CA sing N N 86 LAC C O doub N N 87 LAC C OXT sing N N 88 LAC CA CB sing N N 89 LAC CA OHN sing N N 90 LAC CA HA sing N N 91 LAC CB HB1 sing N N 92 LAC CB HB2 sing N N 93 LAC CB HB3 sing N N 94 LAC OHN H sing N N 95 LAC OXT HXT sing N N 96 MLU N CN sing N N 97 MLU N CA sing N N 98 MLU CA C sing N N 99 MLU CA CB sing N N 100 MLU C O doub N N 101 MLU C OXT sing N N 102 MLU CB CG sing N N 103 MLU CG CD1 sing N N 104 MLU CG CD2 sing N N 105 MLU N H sing N N 106 MLU CN HCN1 sing N N 107 MLU CN HCN2 sing N N 108 MLU CN HCN3 sing N N 109 MLU CA HA sing N N 110 MLU CB HB2 sing N N 111 MLU CB HB3 sing N N 112 MLU OXT HXT sing N N 113 MLU CG HG sing N N 114 MLU CD1 HD11 sing N N 115 MLU CD1 HD12 sing N N 116 MLU CD1 HD13 sing N N 117 MLU CD2 HD21 sing N N 118 MLU CD2 HD22 sing N N 119 MLU CD2 HD23 sing N N 120 OMY N CA sing N N 121 OMY OCZ CZ sing N N 122 OMY CZ CE2 sing Y N 123 OMY CZ CE1 doub Y N 124 OMY CE2 CD2 doub Y N 125 OMY CD2 CG sing Y N 126 OMY CG CD1 doub Y N 127 OMY CG CB sing N N 128 OMY CD1 CE1 sing Y N 129 OMY CE1 CL sing N N 130 OMY C O doub N N 131 OMY C CA sing N N 132 OMY C OXT sing N N 133 OMY CA CB sing N N 134 OMY CB ODE sing N N 135 OMY N H sing N N 136 OMY N H2 sing N N 137 OMY CA HA sing N N 138 OMY OCZ HCZ sing N N 139 OMY CE2 HE2 sing N N 140 OMY CD2 HD2 sing N N 141 OMY CD1 HD1 sing N N 142 OMY CB HB sing N N 143 OMY OXT HXT sing N N 144 OMY ODE HDE sing N N 145 OMZ N CA sing N N 146 OMZ CA C sing N N 147 OMZ CA CB sing N N 148 OMZ C O doub N N 149 OMZ C OXT sing N N 150 OMZ CL CE1 sing N N 151 OMZ CB OC sing N N 152 OMZ CB CG sing N N 153 OMZ CG CD1 doub Y N 154 OMZ CG CD2 sing Y N 155 OMZ CD1 CE1 sing Y N 156 OMZ CD2 CE2 doub Y N 157 OMZ CE1 CZ doub Y N 158 OMZ CE2 CZ sing Y N 159 OMZ CZ OH sing N N 160 OMZ N H sing N N 161 OMZ N H2 sing N N 162 OMZ CA HA sing N N 163 OMZ CB HB sing N N 164 OMZ OXT HXT sing N N 165 OMZ OC HC sing N N 166 OMZ CD1 HD1 sing N N 167 OMZ CD2 HD2 sing N N 168 OMZ CE2 HE2 sing N N 169 OMZ OH HH sing N N 170 RER C1 C2 sing N N 171 RER C1 O5 sing N N 172 RER C1 O1 sing N N 173 RER C2 C3 sing N N 174 RER C3 N3 sing N N 175 RER C3 C3A sing N N 176 RER C3 C4 sing N N 177 RER C4 O4 sing N N 178 RER C4 C5 sing N N 179 RER C5 O5 sing N N 180 RER C5 C5A sing N N 181 RER C1 H1 sing N N 182 RER C2 H21C sing N N 183 RER C2 H22C sing N N 184 RER O1 HO1 sing N N 185 RER N3 H31N sing N N 186 RER N3 H32N sing N N 187 RER C3A H3A1 sing N N 188 RER C3A H3A2 sing N N 189 RER C3A H3A3 sing N N 190 RER C4 H4 sing N N 191 RER O4 HO4 sing N N 192 RER C5 H5 sing N N 193 RER C5A H5A1 sing N N 194 RER C5A H5A2 sing N N 195 RER C5A H5A3 sing N N 196 # 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 'CHLORIDE ION' CL 4 'LACTIC ACID' LAC 5 water HOH #