data_1AA5 # _entry.id 1AA5 # _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 1AA5 pdb_00001aa5 10.2210/pdb1aa5/pdb WWPDB D_1000170583 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1C0Q unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH 2-ACETOXY-D-PROPANOIC ACID' PDB 1C0R unspecified 'CRYSTAL STRUCTURE OF VANCOMYCIN WITH D-LACTIC 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.status_code REL _pdbx_database_status.entry_id 1AA5 _pdbx_database_status.recvd_initial_deposition_date 1997-01-23 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _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 'Bevivino, A.E.' 2 'Korty, B.D.' 3 'Axelsen, P.H.' 4 # _citation.id primary _citation.title ;Simultaneous Recognition of a Carboxylate-Containing Ligand and an Intramolecular Surrogate Ligand in the Crystal Structure of an Asymmetric Vancomycin Dimer. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 119 _citation.page_first 1516 _citation.page_last ? _citation.year 1997 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI 10.1021/JA963566P # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Loll, P.J.' 1 ? primary 'Bevivino, A.E.' 2 ? primary 'Korty, B.D.' 3 ? primary 'Axelsen, P.H.' 4 ? # _cell.entry_id 1AA5 _cell.length_a 28.450 _cell.length_b 28.450 _cell.length_c 65.840 _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 1AA5 _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 syn VANCOMYCIN 1149.977 2 ? ? ? ? 2 branched man 'vancosamine-(1-2)-beta-D-glucopyranose' 323.340 2 ? ? ? ? 3 non-polymer syn 'ACETIC ACID' 60.052 1 ? ? ? ? 4 non-polymer syn 'CHLORIDE ION' 35.453 4 ? ? ? ? 5 water nat water 18.015 55 ? ? ? ? # _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 # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'AMYCOLATOPSIS ORIENTALIS' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 31958 _pdbx_entity_src_syn.details ? # _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 1AA5 A 1 ? 7 ? NOR00681 1 ? 7 ? 1 7 2 1 1AA5 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 ACY non-polymer . 'ACETIC ACID' ? 'C2 H4 O2' 60.052 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 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 1AA5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.90 _exptl_crystal.density_percent_sol 57.53 _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 ;CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF A 25 MG/ML VANCOMYCIN SOLUTION AND 2.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.6 (RESERVOIR BUFFER) AND THEN SUSPENDING THIS DROP OVER THE RESERVOIR. CRYSTALS WERE GROWN AT 293 K., VAPOR DIFFUSION - HANGING DROP ; # _diffrn.id 1 _diffrn.ambient_temp 98 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type ADSC _diffrn_detector.pdbx_collection_date 1996-04 _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 ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.85 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X8C' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X8C _diffrn_source.pdbx_wavelength 0.85 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 1AA5 _reflns.observed_criterion_sigma_I 2.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 10.000 _reflns.d_resolution_high 0.890 _reflns.number_obs 17899 _reflns.number_all ? _reflns.percent_possible_obs 85.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.07600 _reflns.pdbx_netI_over_sigmaI 100.0000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 12.800 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 0.89 _reflns_shell.d_res_low 0.95 _reflns_shell.percent_possible_all 69.3 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.14300 _reflns_shell.meanI_over_sigI_obs 31.500 _reflns_shell.pdbx_redundancy 5.60 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 1AA5 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 17899 _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 4.00 _refine.ls_d_res_high 0.89 _refine.ls_percent_reflns_obs 80.0 _refine.ls_R_factor_obs 0.124 _refine.ls_R_factor_all 0.124 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _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 ? _refine.ls_number_parameters 2553 _refine.ls_number_restraints 3647 _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 ? _refine.details ;REFINEMENT WAS CARRIED OUT VS. F**2; SIMILAR 1,2 AND 1,3 DISTANCE RESTRAINTS WERE APPLIED TO THE TWO VANCOMYCIN MOLECULES. ALSO, RESTRAINTS WERE IMPOSED TO LIMIT DEVIATIONS OF RINGS AND PEPTIDE BONDS FROM PLANARITY AND DIFFERENCES IN ALONG-BOND COMPONENTS OF ADPS. ADPS FOR SOLVENT WERE RESTRAINED TO BE APPROXIMATELY ISOTROPIC, AND ANTIBUMPING RESTRAINTS WERE USED TO PREVENT SOLVENT WATER MOLECULES FROM VIOLATING MINIMUM CONTACT DISTANCES. CONJUGATE GRADIENT LEAST SQUARES WAS USED FOR MOST OF THE REFINEMENT, WITH BLOCKED LEAST SQUARES AT THE END. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'DIRECT METHODS' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _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_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.entry_id 1AA5 _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 3 _refine_analyze.occupancy_sum_hydrogen 158.00 _refine_analyze.occupancy_sum_non_hydrogen 255.40 # _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 50 _refine_hist.number_atoms_solvent 55 _refine_hist.number_atoms_total 265 _refine_hist.d_res_high 0.89 _refine_hist.d_res_low 4.00 # 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 ? ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.019 ? ? ? '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 0.008 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.011 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.025 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 1AA5 _pdbx_refine.R_factor_all_no_cutoff 0.124 _pdbx_refine.R_factor_obs_no_cutoff 0.124 _pdbx_refine.free_R_factor_no_cutoff ? _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 ? _pdbx_refine.R_factor_all_4sig_cutoff 0.112 _pdbx_refine.R_factor_obs_4sig_cutoff 0.112 _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 17479 # _struct.entry_id 1AA5 _struct.title VANCOMYCIN _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1AA5 _struct_keywords.pdbx_keywords ANTIBIOTIC _struct_keywords.text '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 4 ? G N N 4 ? H N N 4 ? I N N 4 ? J N N 5 ? K 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 ? ? ? ? ? ? ? 1.352 ? ? covale2 covale both ? A OMZ 2 C ? ? ? 1_555 A ASN 3 N ? ? A OMZ 2 A ASN 3 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale3 covale none ? A OMZ 2 OH ? ? ? 1_555 A GHP 4 C5 ? ? A OMZ 2 A GHP 4 1_555 ? ? ? ? ? ? ? 1.389 ? ? covale4 covale both ? A ASN 3 C ? ? ? 1_555 A GHP 4 N ? ? A ASN 3 A GHP 4 1_555 ? ? ? ? ? ? ? 1.319 ? ? covale5 covale both ? A GHP 4 C ? ? ? 1_555 A GHP 5 N ? ? A GHP 4 A GHP 5 1_555 ? ? ? ? ? ? ? 1.355 ? ? covale6 covale none ? A GHP 4 C3 ? ? ? 1_555 A OMY 6 OCZ ? ? A GHP 4 A OMY 6 1_555 ? ? ? ? ? ? ? 1.394 ? ? covale7 covale one ? A GHP 4 O4 ? ? ? 1_555 C BGC . C1 ? ? A GHP 4 C BGC 1 1_555 ? ? ? ? ? ? ? 1.414 ? ? covale8 covale both ? A GHP 5 C ? ? ? 1_555 A OMY 6 N ? ? A GHP 5 A OMY 6 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale9 covale one ? A GHP 5 C3 ? ? ? 1_555 A 3FG 7 CG1 ? ? A GHP 5 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.499 ? ? covale10 covale both ? A OMY 6 C ? ? ? 1_555 A 3FG 7 N ? ? A OMY 6 A 3FG 7 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale11 covale both ? B MLU 1 C ? ? ? 1_555 B OMZ 2 N ? ? B MLU 1 B OMZ 2 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale12 covale both ? B OMZ 2 C ? ? ? 1_555 B ASN 3 N ? ? B OMZ 2 B ASN 3 1_555 ? ? ? ? ? ? ? 1.316 ? ? covale13 covale none ? B OMZ 2 OH ? ? ? 1_555 B GHP 4 C5 ? ? B OMZ 2 B GHP 4 1_555 ? ? ? ? ? ? ? 1.395 ? ? covale14 covale both ? B ASN 3 C ? ? ? 1_555 B GHP 4 N ? ? B ASN 3 B GHP 4 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale15 covale both ? B GHP 4 C ? ? ? 1_555 B GHP 5 N ? ? B GHP 4 B GHP 5 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale16 covale none ? B GHP 4 C3 ? ? ? 1_555 B OMY 6 OCZ ? ? B GHP 4 B OMY 6 1_555 ? ? ? ? ? ? ? 1.383 ? ? covale17 covale one ? B GHP 4 O4 B ? ? 1_555 D BGC . C1 B ? B GHP 4 D BGC 1 1_555 ? ? ? ? ? ? ? 1.446 ? ? covale18 covale one ? B GHP 4 O4 A ? ? 1_555 D BGC . C1 A ? B GHP 4 D BGC 1 1_555 ? ? ? ? ? ? ? 1.414 ? ? covale19 covale both ? B GHP 5 C ? ? ? 1_555 B OMY 6 N ? ? B GHP 5 B OMY 6 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale20 covale one ? B GHP 5 C3 ? ? ? 1_555 B 3FG 7 CG1 ? ? B GHP 5 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.505 ? ? covale21 covale both ? B OMY 6 C ? ? ? 1_555 B 3FG 7 N ? ? B OMY 6 B 3FG 7 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale22 covale both ? C BGC . O2 ? ? ? 1_555 C RER . C1 ? ? C BGC 1 C RER 2 1_555 ? ? ? ? ? ? ? 1.406 ? ? covale23 covale both ? D BGC . O2 B ? ? 1_555 D RER . C1 ? ? D BGC 1 D RER 2 1_555 ? ? ? ? ? ? ? 1.099 ? ? covale24 covale both ? D BGC . O2 A ? ? 1_555 D RER . C1 ? ? D BGC 1 D RER 2 1_555 ? ? ? ? ? ? ? 1.466 ? ? # _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 6.04 2 GHP 5 B . ? GHP 5 B OMY 6 B ? OMY 6 B 1 18.86 # _database_PDB_matrix.entry_id 1AA5 _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 1AA5 _atom_sites.fract_transf_matrix[1][1] 0.035149 _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] 0.035149 _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] 0.015188 _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 H N O # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 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 ACY 1 11 11 ACY ACY A . F 4 CL 1 21 21 CL CL A . G 4 CL 1 22 22 CL CL A . H 4 CL 1 21 21 CL CL B . I 4 CL 1 22 22 CL CL B . J 5 HOH 1 2001 2001 HOH HOH A . J 5 HOH 2 2002 2002 HOH HOH A . J 5 HOH 3 2003 2003 HOH HOH A . J 5 HOH 4 2004 2004 HOH HOH A . J 5 HOH 5 2005 2005 HOH HOH A . J 5 HOH 6 2006 2006 HOH HOH A . J 5 HOH 7 2007 2007 HOH HOH A . J 5 HOH 8 2008 2008 HOH HOH A . J 5 HOH 9 2009 2009 HOH HOH A . J 5 HOH 10 2010 2010 HOH HOH A . J 5 HOH 11 2011 2011 HOH HOH A . J 5 HOH 12 2012 2012 HOH HOH A . J 5 HOH 13 2013 2013 HOH HOH A . J 5 HOH 14 2014 2014 HOH HOH A . J 5 HOH 15 2015 2015 HOH HOH A . J 5 HOH 16 2016 2016 HOH HOH A . J 5 HOH 17 2017 2017 HOH HOH A . J 5 HOH 18 2018 2018 HOH HOH A . J 5 HOH 19 2019 2019 HOH HOH A . J 5 HOH 20 2020 2020 HOH HOH A . J 5 HOH 21 2021 2021 HOH HOH A . J 5 HOH 22 2022 2022 HOH HOH A . J 5 HOH 23 2023 2023 HOH HOH A . J 5 HOH 24 2024 2024 HOH HOH A . J 5 HOH 25 2025 2025 HOH HOH A . J 5 HOH 26 2026 2026 HOH HOH A . J 5 HOH 27 2027 2027 HOH HOH A . J 5 HOH 28 2028 2028 HOH HOH A . J 5 HOH 29 2029 2029 HOH HOH A . J 5 HOH 30 2030 2030 HOH HOH A . J 5 HOH 31 2031 2031 HOH HOH A . J 5 HOH 32 2032 2032 HOH HOH A . J 5 HOH 33 2033 2033 HOH HOH A . J 5 HOH 34 2034 2034 HOH HOH A . K 5 HOH 1 2001 2001 HOH HOH B . K 5 HOH 2 2002 2002 HOH HOH B . K 5 HOH 3 2003 2003 HOH HOH B . K 5 HOH 4 2004 2004 HOH HOH B . K 5 HOH 5 2005 2005 HOH HOH B . K 5 HOH 6 2006 2006 HOH HOH B . K 5 HOH 7 2007 2007 HOH HOH B . K 5 HOH 8 2008 2008 HOH HOH B . K 5 HOH 9 2009 2009 HOH HOH B . K 5 HOH 10 2010 2010 HOH HOH B . K 5 HOH 11 2011 2011 HOH HOH B . K 5 HOH 12 2012 2012 HOH HOH B . K 5 HOH 13 2013 2013 HOH HOH B . K 5 HOH 14 2014 2014 HOH HOH B . K 5 HOH 15 2015 2015 HOH HOH B . K 5 HOH 16 2016 2016 HOH HOH B . K 5 HOH 17 2017 2017 HOH HOH B . K 5 HOH 18 2018 2018 HOH HOH B . K 5 HOH 19 2019 2019 HOH HOH B . K 5 HOH 20 2020 2020 HOH HOH B . K 5 HOH 21 2021 2021 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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # 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,F,G,J 1 2 B,D,H,I,K # 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)' 1370 ? 1 MORE -32.8 ? 1 'SSA (A^2)' 2890 ? # 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 '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 2 'crystal symmetry operation' 3_554 -y+1/2,x+1/2,z-1/4 0.0000000000 -1.0000000000 0.0000000000 14.2250000000 1.0000000000 0.0000000000 0.0000000000 14.2250000000 0.0000000000 0.0000000000 1.0000000000 -16.4600000000 # _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 2015 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id J _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 1997-08-20 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' 1 5 2016-10-19 7 'Structure model' 2 0 2020-07-29 8 '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 7 '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' Other 10 7 'Structure model' Advisory 11 7 'Structure model' 'Atomic model' 12 7 'Structure model' 'Data collection' 13 7 'Structure model' 'Derived calculations' 14 7 'Structure model' Other 15 7 'Structure model' 'Polymer sequence' 16 7 'Structure model' 'Structure summary' 17 8 'Structure model' 'Atomic model' 18 8 'Structure model' 'Data collection' 19 8 'Structure model' 'Database references' 20 8 'Structure model' 'Derived calculations' 21 8 '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 7 'Structure model' atom_site 2 7 'Structure model' chem_comp 3 7 'Structure model' entity 4 7 'Structure model' entity_poly 5 7 'Structure model' pdbx_branch_scheme 6 7 'Structure model' pdbx_chem_comp_identifier 7 7 'Structure model' pdbx_database_status 8 7 'Structure model' pdbx_entity_branch 9 7 'Structure model' pdbx_entity_branch_descriptor 10 7 'Structure model' pdbx_entity_branch_link 11 7 'Structure model' pdbx_entity_branch_list 12 7 'Structure model' pdbx_entity_nonpoly 13 7 'Structure model' pdbx_molecule 14 7 'Structure model' pdbx_nonpoly_scheme 15 7 'Structure model' pdbx_struct_assembly 16 7 'Structure model' pdbx_struct_assembly_gen 17 7 'Structure model' pdbx_struct_special_symmetry 18 7 'Structure model' pdbx_validate_close_contact 19 7 'Structure model' struct_asym 20 7 'Structure model' struct_conn 21 7 'Structure model' struct_site 22 7 'Structure model' struct_site_gen 23 8 'Structure model' atom_site 24 8 'Structure model' chem_comp 25 8 'Structure model' chem_comp_atom 26 8 'Structure model' chem_comp_bond 27 8 'Structure model' database_2 28 8 '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 7 'Structure model' '_atom_site.B_iso_or_equiv' 2 7 'Structure model' '_atom_site.Cartn_x' 3 7 'Structure model' '_atom_site.Cartn_y' 4 7 'Structure model' '_atom_site.Cartn_z' 5 7 'Structure model' '_atom_site.auth_asym_id' 6 7 'Structure model' '_atom_site.auth_atom_id' 7 7 'Structure model' '_atom_site.auth_comp_id' 8 7 'Structure model' '_atom_site.auth_seq_id' 9 7 'Structure model' '_atom_site.label_alt_id' 10 7 'Structure model' '_atom_site.label_asym_id' 11 7 'Structure model' '_atom_site.label_atom_id' 12 7 'Structure model' '_atom_site.label_comp_id' 13 7 'Structure model' '_atom_site.label_entity_id' 14 7 'Structure model' '_atom_site.occupancy' 15 7 'Structure model' '_atom_site.type_symbol' 16 7 'Structure model' '_chem_comp.name' 17 7 'Structure model' '_chem_comp.type' 18 7 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 19 7 'Structure model' '_pdbx_database_status.process_site' 20 7 'Structure model' '_pdbx_struct_assembly.method_details' 21 7 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 22 7 'Structure model' '_pdbx_struct_special_symmetry.label_asym_id' 23 7 'Structure model' '_pdbx_validate_close_contact.auth_asym_id_1' 24 7 'Structure model' '_pdbx_validate_close_contact.auth_asym_id_2' 25 7 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_1' 26 7 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_2' 27 7 'Structure model' '_struct_conn.pdbx_dist_value' 28 7 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 29 7 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 30 7 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 31 7 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 32 7 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 33 7 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 34 7 'Structure model' '_struct_conn.ptnr1_label_asym_id' 35 7 'Structure model' '_struct_conn.ptnr1_label_atom_id' 36 7 'Structure model' '_struct_conn.ptnr1_label_comp_id' 37 7 'Structure model' '_struct_conn.ptnr1_label_seq_id' 38 7 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 39 7 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 40 7 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 41 7 'Structure model' '_struct_conn.ptnr2_label_asym_id' 42 7 'Structure model' '_struct_conn.ptnr2_label_atom_id' 43 7 'Structure model' '_struct_conn.ptnr2_label_comp_id' 44 7 'Structure model' '_struct_conn.ptnr2_label_seq_id' 45 8 'Structure model' '_atom_site.auth_atom_id' 46 8 'Structure model' '_atom_site.label_atom_id' 47 8 'Structure model' '_chem_comp.pdbx_synonyms' 48 8 'Structure model' '_database_2.pdbx_DOI' 49 8 'Structure model' '_database_2.pdbx_database_accession' 50 8 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL-93 'model building' . ? 1 SHELXL-93 refinement . ? 2 MADNES 'data reduction' . ? 3 PROCOR 'data reduction' . ? 4 XSCALE 'data scaling' . ? 5 SHELXL-93 phasing . ? 6 # _pdbx_entry_details.entry_id 1AA5 _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 TOGETHER 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 ? ? 2.01 2 1 C2 D BGC 1 ? B C1 D RER 2 ? ? 2.18 # _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 -100.65 _pdbx_validate_torsion.psi -69.08 # 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 ACY C C N N 23 ACY O O N N 24 ACY OXT O N N 25 ACY CH3 C N N 26 ACY HXT H N N 27 ACY H1 H N N 28 ACY H2 H N N 29 ACY H3 H N N 30 ASN N N N N 31 ASN CA C N S 32 ASN C C N N 33 ASN O O N N 34 ASN CB C N N 35 ASN CG C N N 36 ASN OD1 O N N 37 ASN ND2 N N N 38 ASN OXT O N N 39 ASN H H N N 40 ASN H2 H N N 41 ASN HA H N N 42 ASN HB2 H N N 43 ASN HB3 H N N 44 ASN HD21 H N N 45 ASN HD22 H N N 46 ASN HXT H N N 47 BGC C2 C N R 48 BGC C3 C N S 49 BGC C4 C N S 50 BGC C5 C N R 51 BGC C6 C N N 52 BGC C1 C N R 53 BGC O1 O N N 54 BGC O2 O N N 55 BGC O3 O N N 56 BGC O4 O N N 57 BGC O5 O N N 58 BGC O6 O N N 59 BGC H2 H N N 60 BGC H3 H N N 61 BGC H4 H N N 62 BGC H5 H N N 63 BGC H61 H N N 64 BGC H62 H N N 65 BGC H1 H N N 66 BGC HO1 H N N 67 BGC HO2 H N N 68 BGC HO3 H N N 69 BGC HO4 H N N 70 BGC HO6 H N N 71 CL CL CL N N 72 GHP N N N N 73 GHP CA C N R 74 GHP C C N N 75 GHP O O N N 76 GHP OXT O N N 77 GHP C1 C Y N 78 GHP C2 C Y N 79 GHP C3 C Y N 80 GHP C4 C Y N 81 GHP O4 O N N 82 GHP C5 C Y N 83 GHP C6 C Y N 84 GHP H H N N 85 GHP H2 H N N 86 GHP HA H N N 87 GHP HXT H N N 88 GHP HC2 H N N 89 GHP H3 H N N 90 GHP HO4 H N N 91 GHP H5 H N N 92 GHP H6 H N N 93 HOH O O N N 94 HOH H1 H N N 95 HOH H2 H N N 96 MLU N N N N 97 MLU CN C N N 98 MLU CA C N R 99 MLU C C N N 100 MLU O O N N 101 MLU CB C N N 102 MLU CG C N N 103 MLU CD1 C N N 104 MLU CD2 C N N 105 MLU OXT O N N 106 MLU H H N N 107 MLU HCN1 H N N 108 MLU HCN2 H N N 109 MLU HCN3 H N N 110 MLU HA H N N 111 MLU HB2 H N N 112 MLU HB3 H N N 113 MLU HXT H N N 114 MLU HG H N N 115 MLU HD11 H N N 116 MLU HD12 H N N 117 MLU HD13 H N N 118 MLU HD21 H N N 119 MLU HD22 H N N 120 MLU HD23 H N N 121 OMY N N N N 122 OMY CA C N S 123 OMY OCZ O N N 124 OMY CE2 C Y N 125 OMY CE1 C Y N 126 OMY CZ C Y N 127 OMY CG C Y N 128 OMY CD2 C Y N 129 OMY CD1 C Y N 130 OMY CB C N R 131 OMY CL CL N N 132 OMY O O N N 133 OMY C C N N 134 OMY ODE O N N 135 OMY OXT O N N 136 OMY H H N N 137 OMY H2 H N N 138 OMY HA H N N 139 OMY HCZ H N N 140 OMY HE2 H N N 141 OMY HD2 H N N 142 OMY HD1 H N N 143 OMY HB H N N 144 OMY HXT H N N 145 OMY HDE H N N 146 OMZ N N N N 147 OMZ CA C N R 148 OMZ C C N N 149 OMZ O O N N 150 OMZ OXT O N N 151 OMZ CB C N R 152 OMZ OC O N N 153 OMZ CG C Y N 154 OMZ CD1 C Y N 155 OMZ CD2 C Y N 156 OMZ CE1 C Y N 157 OMZ CL CL N N 158 OMZ CE2 C Y N 159 OMZ CZ C Y N 160 OMZ OH O N N 161 OMZ H H N N 162 OMZ H2 H N N 163 OMZ HA H N N 164 OMZ HB H N N 165 OMZ HXT H N N 166 OMZ HC H N N 167 OMZ HD1 H N N 168 OMZ HD2 H N N 169 OMZ HE2 H N N 170 OMZ HH H N N 171 RER C1 C N R 172 RER C2 C N N 173 RER C3 C N S 174 RER N3 N N N 175 RER C3A C N N 176 RER C4 C N S 177 RER O4 O N N 178 RER C5 C N S 179 RER O5 O N N 180 RER C5A C N N 181 RER O1 O N N 182 RER H1 H N N 183 RER H21C H N N 184 RER H22C H N N 185 RER HO1 H N N 186 RER H31N H N N 187 RER H32N H N N 188 RER H3A1 H N N 189 RER H3A2 H N N 190 RER H3A3 H N N 191 RER H4 H N N 192 RER HO4 H N N 193 RER H5 H N N 194 RER H5A1 H N N 195 RER H5A2 H N N 196 RER H5A3 H N N 197 # 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 ACY C O doub N N 23 ACY C OXT sing N N 24 ACY C CH3 sing N N 25 ACY OXT HXT sing N N 26 ACY CH3 H1 sing N N 27 ACY CH3 H2 sing N N 28 ACY CH3 H3 sing N N 29 ASN N CA sing N N 30 ASN N H sing N N 31 ASN N H2 sing N N 32 ASN CA C sing N N 33 ASN CA CB sing N N 34 ASN CA HA sing N N 35 ASN C O doub N N 36 ASN C OXT sing N N 37 ASN CB CG sing N N 38 ASN CB HB2 sing N N 39 ASN CB HB3 sing N N 40 ASN CG OD1 doub N N 41 ASN CG ND2 sing N N 42 ASN ND2 HD21 sing N N 43 ASN ND2 HD22 sing N N 44 ASN OXT HXT sing N N 45 BGC C2 C3 sing N N 46 BGC C2 C1 sing N N 47 BGC C2 O2 sing N N 48 BGC C2 H2 sing N N 49 BGC C3 C4 sing N N 50 BGC C3 O3 sing N N 51 BGC C3 H3 sing N N 52 BGC C4 C5 sing N N 53 BGC C4 O4 sing N N 54 BGC C4 H4 sing N N 55 BGC C5 C6 sing N N 56 BGC C5 O5 sing N N 57 BGC C5 H5 sing N N 58 BGC C6 O6 sing N N 59 BGC C6 H61 sing N N 60 BGC C6 H62 sing N N 61 BGC C1 O1 sing N N 62 BGC C1 O5 sing N N 63 BGC C1 H1 sing N N 64 BGC O1 HO1 sing N N 65 BGC O2 HO2 sing N N 66 BGC O3 HO3 sing N N 67 BGC O4 HO4 sing N N 68 BGC O6 HO6 sing N N 69 GHP N CA sing N N 70 GHP N H sing N N 71 GHP N H2 sing N N 72 GHP CA C sing N N 73 GHP CA C1 sing N N 74 GHP CA HA sing N N 75 GHP C O doub N N 76 GHP C OXT sing N N 77 GHP OXT HXT sing N N 78 GHP C1 C2 doub Y N 79 GHP C1 C6 sing Y N 80 GHP C2 C3 sing Y N 81 GHP C2 HC2 sing N N 82 GHP C3 C4 doub Y N 83 GHP C3 H3 sing N N 84 GHP C4 O4 sing N N 85 GHP C4 C5 sing Y N 86 GHP O4 HO4 sing N N 87 GHP C5 C6 doub Y N 88 GHP C5 H5 sing N N 89 GHP C6 H6 sing N N 90 HOH O H1 sing N N 91 HOH O H2 sing N N 92 MLU N CN sing N N 93 MLU N CA sing N N 94 MLU CA C sing N N 95 MLU CA CB sing N N 96 MLU C O doub N N 97 MLU C OXT sing N N 98 MLU CB CG sing N N 99 MLU CG CD1 sing N N 100 MLU CG CD2 sing N N 101 MLU N H sing N N 102 MLU CN HCN1 sing N N 103 MLU CN HCN2 sing N N 104 MLU CN HCN3 sing N N 105 MLU CA HA sing N N 106 MLU CB HB2 sing N N 107 MLU CB HB3 sing N N 108 MLU OXT HXT sing N N 109 MLU CG HG sing N N 110 MLU CD1 HD11 sing N N 111 MLU CD1 HD12 sing N N 112 MLU CD1 HD13 sing N N 113 MLU CD2 HD21 sing N N 114 MLU CD2 HD22 sing N N 115 MLU CD2 HD23 sing N N 116 OMY N CA sing N N 117 OMY OCZ CZ sing N N 118 OMY CZ CE2 sing Y N 119 OMY CZ CE1 doub Y N 120 OMY CE2 CD2 doub Y N 121 OMY CD2 CG sing Y N 122 OMY CG CD1 doub Y N 123 OMY CG CB sing N N 124 OMY CD1 CE1 sing Y N 125 OMY CE1 CL sing N N 126 OMY C O doub N N 127 OMY C CA sing N N 128 OMY C OXT sing N N 129 OMY CA CB sing N N 130 OMY CB ODE sing N N 131 OMY N H sing N N 132 OMY N H2 sing N N 133 OMY CA HA sing N N 134 OMY OCZ HCZ sing N N 135 OMY CE2 HE2 sing N N 136 OMY CD2 HD2 sing N N 137 OMY CD1 HD1 sing N N 138 OMY CB HB sing N N 139 OMY OXT HXT sing N N 140 OMY ODE HDE sing N N 141 OMZ N CA sing N N 142 OMZ CA C sing N N 143 OMZ CA CB sing N N 144 OMZ C O doub N N 145 OMZ C OXT sing N N 146 OMZ CL CE1 sing N N 147 OMZ CB OC sing N N 148 OMZ CB CG sing N N 149 OMZ CG CD1 doub Y N 150 OMZ CG CD2 sing Y N 151 OMZ CD1 CE1 sing Y N 152 OMZ CD2 CE2 doub Y N 153 OMZ CE1 CZ doub Y N 154 OMZ CE2 CZ sing Y N 155 OMZ CZ OH sing N N 156 OMZ N H sing N N 157 OMZ N H2 sing N N 158 OMZ CA HA sing N N 159 OMZ CB HB sing N N 160 OMZ OXT HXT sing N N 161 OMZ OC HC sing N N 162 OMZ CD1 HD1 sing N N 163 OMZ CD2 HD2 sing N N 164 OMZ CE2 HE2 sing N N 165 OMZ OH HH sing N N 166 RER C1 C2 sing N N 167 RER C1 O5 sing N N 168 RER C1 O1 sing N N 169 RER C2 C3 sing N N 170 RER C3 N3 sing N N 171 RER C3 C3A sing N N 172 RER C3 C4 sing N N 173 RER C4 O4 sing N N 174 RER C4 C5 sing N N 175 RER C5 O5 sing N N 176 RER C5 C5A sing N N 177 RER C1 H1 sing N N 178 RER C2 H21C sing N N 179 RER C2 H22C sing N N 180 RER O1 HO1 sing N N 181 RER N3 H31N sing N N 182 RER N3 H32N sing N N 183 RER C3A H3A1 sing N N 184 RER C3A H3A2 sing N N 185 RER C3A H3A3 sing N N 186 RER C4 H4 sing N N 187 RER O4 HO4 sing N N 188 RER C5 H5 sing N N 189 RER C5A H5A1 sing N N 190 RER C5A H5A2 sing N N 191 RER C5A H5A3 sing N N 192 # 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 'ACETIC ACID' ACY 4 'CHLORIDE ION' CL 5 water HOH #