data_4R9W # _entry.id 4R9W # _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 4R9W RCSB RCSB087082 WWPDB D_1000087082 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4R97 'KKOFab only' unspecified PDB 4R9Y 'KKOFab in complex with platelet factor 4' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4R9W _pdbx_database_status.recvd_initial_deposition_date 2014-09-08 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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.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 'Cai, Z.' 1 'Zhu, Z.' 2 'Liu, Q.' 3 'Greene, M.I.' 4 # _citation.id primary _citation.title 'Atomic description of the immune complex involved in heparin-induced thrombocytopenia.' _citation.journal_abbrev 'Nat Commun' _citation.journal_volume 6 _citation.page_first 8277 _citation.page_last 8277 _citation.year 2015 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 2041-1723 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 26391892 _citation.pdbx_database_id_DOI 10.1038/ncomms9277 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cai, Z.' 1 ? primary 'Yarovoi, S.V.' 2 ? primary 'Zhu, Z.' 3 ? primary 'Rauova, L.' 4 ? primary 'Hayes, V.' 5 ? primary 'Lebedeva, T.' 6 ? primary 'Liu, Q.' 7 ? primary 'Poncz, M.' 8 ? primary 'Arepally, G.' 9 ? primary 'Cines, D.B.' 10 ? primary 'Greene, M.I.' 11 ? # _cell.entry_id 4R9W _cell.length_a 67.333 _cell.length_b 67.333 _cell.length_c 61.756 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4R9W _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? # 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 'Platelet factor 4' 7782.195 2 ? ? ? ? 2 branched man ;2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside ; 1508.264 1 ? ? ? ? 3 water nat water 18.015 17 ? ? ? ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 'PF-4, C-X-C motif chemokine 4, Iroplact, Oncostatin-A, Platelet factor 4, short form' 2 fondaparinux # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code EAEEDGDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES _entity_poly.pdbx_seq_one_letter_code_can EAEEDGDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES _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 GLU n 1 2 ALA n 1 3 GLU n 1 4 GLU n 1 5 ASP n 1 6 GLY n 1 7 ASP n 1 8 LEU n 1 9 GLN n 1 10 CYS n 1 11 LEU n 1 12 CYS n 1 13 VAL n 1 14 LYS n 1 15 THR n 1 16 THR n 1 17 SER n 1 18 GLN n 1 19 VAL n 1 20 ARG n 1 21 PRO n 1 22 ARG n 1 23 HIS n 1 24 ILE n 1 25 THR n 1 26 SER n 1 27 LEU n 1 28 GLU n 1 29 VAL n 1 30 ILE n 1 31 LYS n 1 32 ALA n 1 33 GLY n 1 34 PRO n 1 35 HIS n 1 36 CYS n 1 37 PRO n 1 38 THR n 1 39 ALA n 1 40 GLN n 1 41 LEU n 1 42 ILE n 1 43 ALA n 1 44 THR n 1 45 LEU n 1 46 LYS n 1 47 ASN n 1 48 GLY n 1 49 ARG n 1 50 LYS n 1 51 ILE n 1 52 CYS n 1 53 LEU n 1 54 ASP n 1 55 LEU n 1 56 GLN n 1 57 ALA n 1 58 PRO n 1 59 LEU n 1 60 TYR n 1 61 LYS n 1 62 LYS n 1 63 ILE n 1 64 ILE n 1 65 LYS n 1 66 LYS n 1 67 LEU n 1 68 LEU n 1 69 GLU n 1 70 SER 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 human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'PF4, CXCL4, SCYB4' _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 'Drosophila melanogaster' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 7227 _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 'S2 cells' _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 UNP _struct_ref.db_code PLF4_HUMAN _struct_ref.pdbx_db_accession P02776 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code EAEEDGDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES _struct_ref.pdbx_align_begin 32 _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 4R9W A 1 ? 70 ? P02776 32 ? 101 ? 1 70 2 1 4R9W B 1 ? 70 ? P02776 32 ? 101 ? 101 170 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 BDP 'D-saccharide, beta linking' . 'beta-D-glucopyranuronic acid' 'D-GLUCURONIC ACID' 'C6 H10 O7' 194.139 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 IDS 'L-saccharide, alpha linking' n '2-O-sulfo-alpha-L-idopyranuronic acid' 'O2-SULFO-GLUCURONIC ACID' 'C6 H10 O10 S' 274.203 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 SGN 'D-saccharide, alpha linking' n '2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose' ? 'C6 H13 N O11 S2' 339.298 SUS 'D-saccharide, alpha linking' n '2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose' ? 'C6 H13 N O14 S3' 419.361 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 ZDO D-saccharide n 'methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside' ? 'C7 H15 N O11 S2' 353.324 # _exptl.entry_id 4R9W _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.60 _exptl_crystal.density_percent_sol 52.63 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 289 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '2% PEG4000, 17% MPD, 0.1 M sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K' # _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 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2013-07-28 _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 'Single crystal bender' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9791 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X4C' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X4C _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9791 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4R9W _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 30 _reflns.d_resolution_high 2.50 _reflns.number_obs 5900 _reflns.number_all ? _reflns.percent_possible_obs 98.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.pdbx_chi_squared 1 1 2.50 2.54 98.2 0.689 ? ? 5.3 ? ? ? ? ? ? 1 2 2.54 2.59 97.8 0.492 ? ? 5.6 ? ? ? ? ? ? 1 3 2.59 2.64 99.4 0.478 ? ? 5.7 ? ? ? ? ? ? 1 4 2.64 2.69 99.0 0.462 ? ? 5.8 ? ? ? ? ? ? 1 5 2.69 2.75 100.0 0.410 ? ? 5.8 ? ? ? ? ? ? 1 6 2.75 2.82 99.3 0.250 ? ? 5.8 ? ? ? ? ? ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4R9W _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 5742 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.35 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 22.756 _refine.ls_d_res_high 2.500 _refine.ls_percent_reflns_obs 98.02 _refine.ls_R_factor_obs 0.2244 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2235 _refine.ls_R_factor_R_free 0.2448 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.46 _refine.ls_number_reflns_R_free 256 _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 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _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 0.26 _refine.pdbx_overall_phase_error 32.60 _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.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 973 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 91 _refine_hist.number_atoms_solvent 17 _refine_hist.number_atoms_total 1081 _refine_hist.d_res_high 2.500 _refine_hist.d_res_low 22.756 # 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 f_bond_d 0.006 ? ? 1083 'X-RAY DIFFRACTION' ? f_angle_d 0.928 ? ? 1478 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 25.540 ? ? 452 'X-RAY DIFFRACTION' ? f_chiral_restr 0.532 ? ? 202 'X-RAY DIFFRACTION' ? f_plane_restr 0.004 ? ? 163 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 2.50 3.1489 2715 0.3409 99.00 0.3331 . . 125 . . . . 'X-RAY DIFFRACTION' . 3.1489 22.7570 2771 0.2025 98.00 0.2261 . . 131 . . . . # _struct.entry_id 4R9W _struct.title 'Crystal structure of platelet factor 4 complexed with fondaparinux' _struct.pdbx_descriptor 'Platelet factor 4' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4R9W _struct_keywords.pdbx_keywords CYTOKINE _struct_keywords.text 'PF4, fondaparinux, CXC chemokine, platelet factor, glycosaminoglycan, platelet, CYTOKINE' # 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 3 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ARG A 20 ? ARG A 22 ? ARG A 20 ARG A 22 5 ? 3 HELX_P HELX_P2 2 GLN A 56 ? LEU A 68 ? GLN A 56 LEU A 68 1 ? 13 HELX_P HELX_P3 3 ARG B 20 ? ARG B 22 ? ARG B 120 ARG B 122 5 ? 3 HELX_P HELX_P4 4 PRO B 58 ? SER B 70 ? PRO B 158 SER B 170 1 ? 13 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 disulf1 disulf ? ? A CYS 10 SG ? ? ? 1_555 A CYS 36 SG ? ? A CYS 10 A CYS 36 1_555 ? ? ? ? ? ? ? 2.029 ? ? disulf2 disulf ? ? A CYS 12 SG ? ? ? 1_555 A CYS 52 SG ? ? A CYS 12 A CYS 52 1_555 ? ? ? ? ? ? ? 2.029 ? ? disulf3 disulf ? ? B CYS 10 SG ? ? ? 1_555 B CYS 36 SG ? ? B CYS 110 B CYS 136 1_555 ? ? ? ? ? ? ? 2.029 ? ? disulf4 disulf ? ? B CYS 12 SG ? ? ? 1_555 B CYS 52 SG ? ? B CYS 112 B CYS 152 1_555 ? ? ? ? ? ? ? 2.028 ? ? covale1 covale both ? C ZDO . O4 ? ? ? 1_555 C IDS . C1 ? ? C ZDO 1 C IDS 2 1_555 ? ? ? ? ? ? ? 1.431 sing ? covale2 covale both ? C IDS . O4 ? ? ? 1_555 C SUS . C1 ? ? C IDS 2 C SUS 3 1_555 ? ? ? ? ? ? ? 1.430 sing ? covale3 covale both ? C SUS . O4 ? ? ? 1_555 C BDP . C1 ? ? C SUS 3 C BDP 4 1_555 ? ? ? ? ? ? ? 1.428 sing ? covale4 covale both ? C BDP . O4 ? ? ? 1_555 C SGN . C1 ? ? C BDP 4 C SGN 5 1_555 ? ? ? ? ? ? ? 1.427 sing ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 6 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 LYS A 50 ? CYS A 52 ? LYS A 50 CYS A 52 A 2 GLN A 40 ? LEU A 45 ? GLN A 40 LEU A 45 A 3 ILE A 24 ? ILE A 30 ? ILE A 24 ILE A 30 A 4 ILE B 24 ? ILE B 30 ? ILE B 124 ILE B 130 A 5 GLN B 40 ? LEU B 45 ? GLN B 140 LEU B 145 A 6 LYS B 50 ? CYS B 52 ? LYS B 150 CYS B 152 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O ILE A 51 ? O ILE A 51 N ALA A 43 ? N ALA A 43 A 2 3 O GLN A 40 ? O GLN A 40 N ILE A 30 ? N ILE A 30 A 3 4 N VAL A 29 ? N VAL A 29 O LEU B 27 ? O LEU B 127 A 4 5 N GLU B 28 ? N GLU B 128 O ILE B 42 ? O ILE B 142 A 5 6 N ALA B 43 ? N ALA B 143 O ILE B 51 ? O ILE B 151 # _database_PDB_matrix.entry_id 4R9W _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 4R9W _atom_sites.fract_transf_matrix[1][1] 0.014852 _atom_sites.fract_transf_matrix[1][2] 0.008575 _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] 0.017149 _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] 0.016193 _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 S # 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 GLU 1 1 ? ? ? A . n A 1 2 ALA 2 2 ? ? ? A . n A 1 3 GLU 3 3 ? ? ? A . n A 1 4 GLU 4 4 ? ? ? A . n A 1 5 ASP 5 5 ? ? ? A . n A 1 6 GLY 6 6 ? ? ? A . n A 1 7 ASP 7 7 ? ? ? A . n A 1 8 LEU 8 8 8 LEU LEU A . n A 1 9 GLN 9 9 9 GLN GLN A . n A 1 10 CYS 10 10 10 CYS CYS A . n A 1 11 LEU 11 11 11 LEU LEU A . n A 1 12 CYS 12 12 12 CYS CYS A . n A 1 13 VAL 13 13 13 VAL VAL A . n A 1 14 LYS 14 14 14 LYS LYS A . n A 1 15 THR 15 15 15 THR THR A . n A 1 16 THR 16 16 16 THR THR A . n A 1 17 SER 17 17 17 SER SER A . n A 1 18 GLN 18 18 18 GLN GLN A . n A 1 19 VAL 19 19 19 VAL VAL A . n A 1 20 ARG 20 20 20 ARG ARG A . n A 1 21 PRO 21 21 21 PRO PRO A . n A 1 22 ARG 22 22 22 ARG ARG A . n A 1 23 HIS 23 23 23 HIS HIS A . n A 1 24 ILE 24 24 24 ILE ILE A . n A 1 25 THR 25 25 25 THR THR A . n A 1 26 SER 26 26 26 SER SER A . n A 1 27 LEU 27 27 27 LEU LEU A . n A 1 28 GLU 28 28 28 GLU GLU A . n A 1 29 VAL 29 29 29 VAL VAL A . n A 1 30 ILE 30 30 30 ILE ILE A . n A 1 31 LYS 31 31 31 LYS LYS A . n A 1 32 ALA 32 32 32 ALA ALA A . n A 1 33 GLY 33 33 33 GLY GLY A . n A 1 34 PRO 34 34 34 PRO PRO A . n A 1 35 HIS 35 35 35 HIS HIS A . n A 1 36 CYS 36 36 36 CYS CYS A . n A 1 37 PRO 37 37 37 PRO PRO A . n A 1 38 THR 38 38 38 THR THR A . n A 1 39 ALA 39 39 39 ALA ALA A . n A 1 40 GLN 40 40 40 GLN GLN A . n A 1 41 LEU 41 41 41 LEU LEU A . n A 1 42 ILE 42 42 42 ILE ILE A . n A 1 43 ALA 43 43 43 ALA ALA A . n A 1 44 THR 44 44 44 THR THR A . n A 1 45 LEU 45 45 45 LEU LEU A . n A 1 46 LYS 46 46 46 LYS LYS A . n A 1 47 ASN 47 47 47 ASN ASN A . n A 1 48 GLY 48 48 48 GLY GLY A . n A 1 49 ARG 49 49 49 ARG ARG A . n A 1 50 LYS 50 50 50 LYS LYS A . n A 1 51 ILE 51 51 51 ILE ILE A . n A 1 52 CYS 52 52 52 CYS CYS A . n A 1 53 LEU 53 53 53 LEU LEU A . n A 1 54 ASP 54 54 54 ASP ASP A . n A 1 55 LEU 55 55 55 LEU LEU A . n A 1 56 GLN 56 56 56 GLN GLN A . n A 1 57 ALA 57 57 57 ALA ALA A . n A 1 58 PRO 58 58 58 PRO PRO A . n A 1 59 LEU 59 59 59 LEU LEU A . n A 1 60 TYR 60 60 60 TYR TYR A . n A 1 61 LYS 61 61 61 LYS LYS A . n A 1 62 LYS 62 62 62 LYS LYS A . n A 1 63 ILE 63 63 63 ILE ILE A . n A 1 64 ILE 64 64 64 ILE ILE A . n A 1 65 LYS 65 65 65 LYS LYS A . n A 1 66 LYS 66 66 66 LYS LYS A . n A 1 67 LEU 67 67 67 LEU LEU A . n A 1 68 LEU 68 68 68 LEU LEU A . n A 1 69 GLU 69 69 69 GLU GLU A . n A 1 70 SER 70 70 ? ? ? A . n B 1 1 GLU 1 101 ? ? ? B . n B 1 2 ALA 2 102 ? ? ? B . n B 1 3 GLU 3 103 ? ? ? B . n B 1 4 GLU 4 104 ? ? ? B . n B 1 5 ASP 5 105 ? ? ? B . n B 1 6 GLY 6 106 ? ? ? B . n B 1 7 ASP 7 107 107 ASP ASP B . n B 1 8 LEU 8 108 108 LEU LEU B . n B 1 9 GLN 9 109 109 GLN GLN B . n B 1 10 CYS 10 110 110 CYS CYS B . n B 1 11 LEU 11 111 111 LEU LEU B . n B 1 12 CYS 12 112 112 CYS CYS B . n B 1 13 VAL 13 113 113 VAL VAL B . n B 1 14 LYS 14 114 114 LYS LYS B . n B 1 15 THR 15 115 115 THR THR B . n B 1 16 THR 16 116 116 THR THR B . n B 1 17 SER 17 117 117 SER SER B . n B 1 18 GLN 18 118 118 GLN GLN B . n B 1 19 VAL 19 119 119 VAL VAL B . n B 1 20 ARG 20 120 120 ARG ARG B . n B 1 21 PRO 21 121 121 PRO PRO B . n B 1 22 ARG 22 122 122 ARG ARG B . n B 1 23 HIS 23 123 123 HIS HIS B . n B 1 24 ILE 24 124 124 ILE ILE B . n B 1 25 THR 25 125 125 THR THR B . n B 1 26 SER 26 126 126 SER SER B . n B 1 27 LEU 27 127 127 LEU LEU B . n B 1 28 GLU 28 128 128 GLU GLU B . n B 1 29 VAL 29 129 129 VAL VAL B . n B 1 30 ILE 30 130 130 ILE ILE B . n B 1 31 LYS 31 131 131 LYS LYS B . n B 1 32 ALA 32 132 132 ALA ALA B . n B 1 33 GLY 33 133 133 GLY GLY B . n B 1 34 PRO 34 134 134 PRO PRO B . n B 1 35 HIS 35 135 135 HIS HIS B . n B 1 36 CYS 36 136 136 CYS CYS B . n B 1 37 PRO 37 137 137 PRO PRO B . n B 1 38 THR 38 138 138 THR THR B . n B 1 39 ALA 39 139 139 ALA ALA B . n B 1 40 GLN 40 140 140 GLN GLN B . n B 1 41 LEU 41 141 141 LEU LEU B . n B 1 42 ILE 42 142 142 ILE ILE B . n B 1 43 ALA 43 143 143 ALA ALA B . n B 1 44 THR 44 144 144 THR THR B . n B 1 45 LEU 45 145 145 LEU LEU B . n B 1 46 LYS 46 146 146 LYS LYS B . n B 1 47 ASN 47 147 147 ASN ASN B . n B 1 48 GLY 48 148 148 GLY GLY B . n B 1 49 ARG 49 149 149 ARG ARG B . n B 1 50 LYS 50 150 150 LYS LYS B . n B 1 51 ILE 51 151 151 ILE ILE B . n B 1 52 CYS 52 152 152 CYS CYS B . n B 1 53 LEU 53 153 153 LEU LEU B . n B 1 54 ASP 54 154 154 ASP ASP B . n B 1 55 LEU 55 155 155 LEU LEU B . n B 1 56 GLN 56 156 156 GLN GLN B . n B 1 57 ALA 57 157 157 ALA ALA B . n B 1 58 PRO 58 158 158 PRO PRO B . n B 1 59 LEU 59 159 159 LEU LEU B . n B 1 60 TYR 60 160 160 TYR TYR B . n B 1 61 LYS 61 161 161 LYS LYS B . n B 1 62 LYS 62 162 162 LYS LYS B . n B 1 63 ILE 63 163 163 ILE ILE B . n B 1 64 ILE 64 164 164 ILE ILE B . n B 1 65 LYS 65 165 165 LYS LYS B . n B 1 66 LYS 66 166 166 LYS LYS B . n B 1 67 LEU 67 167 167 LEU LEU B . n B 1 68 LEU 68 168 168 LEU LEU B . n B 1 69 GLU 69 169 169 GLU GLU B . n B 1 70 SER 70 170 170 SER SER 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 D 3 HOH 1 101 1 HOH HOH A . D 3 HOH 2 102 2 HOH HOH A . D 3 HOH 3 103 3 HOH HOH A . D 3 HOH 4 104 4 HOH HOH A . D 3 HOH 5 105 8 HOH HOH A . D 3 HOH 6 106 9 HOH HOH A . D 3 HOH 7 107 11 HOH HOH A . D 3 HOH 8 108 12 HOH HOH A . D 3 HOH 9 109 13 HOH HOH A . D 3 HOH 10 110 14 HOH HOH A . D 3 HOH 11 111 15 HOH HOH A . D 3 HOH 12 112 17 HOH HOH A . E 3 HOH 1 301 5 HOH HOH B . E 3 HOH 2 302 6 HOH HOH B . E 3 HOH 3 303 7 HOH HOH B . E 3 HOH 4 304 10 HOH HOH B . E 3 HOH 5 305 16 HOH HOH B . # _pdbx_molecule_features.prd_id PRD_900028 _pdbx_molecule_features.name fondaparinux _pdbx_molecule_features.type Oligosaccharide _pdbx_molecule_features.class Anticoagulant _pdbx_molecule_features.details oligosaccharide # _pdbx_molecule.instance_id 1 _pdbx_molecule.prd_id PRD_900028 _pdbx_molecule.asym_id C # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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)' 6500 ? 1 MORE -35 ? 1 'SSA (A^2)' 13010 ? # 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' 4_555 y,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2015-12-16 2 'Structure model' 1 1 2016-01-27 3 'Structure model' 1 2 2017-07-12 4 'Structure model' 1 3 2017-11-22 5 'Structure model' 2 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' 'Database references' 2 3 'Structure model' 'Structure summary' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Atomic model' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' 'Non-polymer description' 8 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 4 'Structure model' software 2 5 'Structure model' atom_site 3 5 'Structure model' atom_site_anisotrop 4 5 'Structure model' chem_comp 5 5 'Structure model' entity 6 5 'Structure model' entity_name_com 7 5 'Structure model' pdbx_branch_scheme 8 5 'Structure model' pdbx_chem_comp_identifier 9 5 'Structure model' pdbx_entity_branch 10 5 'Structure model' pdbx_entity_branch_descriptor 11 5 'Structure model' pdbx_entity_branch_link 12 5 'Structure model' pdbx_entity_branch_list 13 5 'Structure model' pdbx_entity_nonpoly 14 5 'Structure model' pdbx_molecule_features 15 5 'Structure model' pdbx_nonpoly_scheme 16 5 'Structure model' struct_conn 17 5 'Structure model' struct_conn_type 18 5 'Structure model' struct_site 19 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 3 'Structure model' '_chem_comp.pdbx_synonyms' 2 4 'Structure model' '_software.name' 3 5 'Structure model' '_atom_site.B_iso_or_equiv' 4 5 'Structure model' '_atom_site.Cartn_x' 5 5 'Structure model' '_atom_site.Cartn_y' 6 5 'Structure model' '_atom_site.Cartn_z' 7 5 'Structure model' '_atom_site.auth_asym_id' 8 5 'Structure model' '_atom_site.auth_atom_id' 9 5 'Structure model' '_atom_site.auth_comp_id' 10 5 'Structure model' '_atom_site.auth_seq_id' 11 5 'Structure model' '_atom_site.label_atom_id' 12 5 'Structure model' '_atom_site.label_comp_id' 13 5 'Structure model' '_atom_site.type_symbol' 14 5 'Structure model' '_atom_site_anisotrop.U[1][1]' 15 5 'Structure model' '_atom_site_anisotrop.U[1][2]' 16 5 'Structure model' '_atom_site_anisotrop.U[1][3]' 17 5 'Structure model' '_atom_site_anisotrop.U[2][2]' 18 5 'Structure model' '_atom_site_anisotrop.U[2][3]' 19 5 'Structure model' '_atom_site_anisotrop.U[3][3]' 20 5 'Structure model' '_atom_site_anisotrop.pdbx_auth_asym_id' 21 5 'Structure model' '_atom_site_anisotrop.pdbx_auth_atom_id' 22 5 'Structure model' '_atom_site_anisotrop.pdbx_auth_comp_id' 23 5 'Structure model' '_atom_site_anisotrop.pdbx_auth_seq_id' 24 5 'Structure model' '_atom_site_anisotrop.pdbx_label_atom_id' 25 5 'Structure model' '_atom_site_anisotrop.pdbx_label_comp_id' 26 5 'Structure model' '_atom_site_anisotrop.type_symbol' 27 5 'Structure model' '_chem_comp.formula' 28 5 'Structure model' '_chem_comp.formula_weight' 29 5 'Structure model' '_chem_comp.id' 30 5 'Structure model' '_chem_comp.mon_nstd_flag' 31 5 'Structure model' '_chem_comp.name' 32 5 'Structure model' '_chem_comp.pdbx_synonyms' 33 5 'Structure model' '_chem_comp.type' 34 5 'Structure model' '_entity.formula_weight' 35 5 'Structure model' '_entity.pdbx_description' 36 5 'Structure model' '_entity.src_method' 37 5 'Structure model' '_entity.type' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 17.4423 _pdbx_refine_tls.origin_y 20.9149 _pdbx_refine_tls.origin_z 8.2694 _pdbx_refine_tls.T[1][1] 0.3722 _pdbx_refine_tls.T[2][2] 0.6502 _pdbx_refine_tls.T[3][3] 0.4423 _pdbx_refine_tls.T[1][2] -0.0072 _pdbx_refine_tls.T[1][3] -0.0627 _pdbx_refine_tls.T[2][3] 0.0908 _pdbx_refine_tls.L[1][1] 4.9819 _pdbx_refine_tls.L[2][2] 5.9353 _pdbx_refine_tls.L[3][3] 3.7957 _pdbx_refine_tls.L[1][2] -0.4018 _pdbx_refine_tls.L[1][3] 1.1796 _pdbx_refine_tls.L[2][3] 0.2278 _pdbx_refine_tls.S[1][1] 0.2163 _pdbx_refine_tls.S[1][2] -1.0576 _pdbx_refine_tls.S[1][3] -0.4224 _pdbx_refine_tls.S[2][1] 0.4320 _pdbx_refine_tls.S[2][2] 0.1495 _pdbx_refine_tls.S[2][3] -0.2469 _pdbx_refine_tls.S[3][1] 0.2740 _pdbx_refine_tls.S[3][2] 0.1713 _pdbx_refine_tls.S[3][3] 0.0657 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id ? _pdbx_refine_tls_group.beg_auth_seq_id ? _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id ? _pdbx_refine_tls_group.end_auth_seq_id ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details all # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345 'data collection' . ? 1 MOLREP phasing . ? 2 PHENIX refinement '(phenix.refine: 1.8.1_1168)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # 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 CYS A 12 ? ? -104.74 77.39 2 1 VAL A 13 ? ? -65.86 -82.67 3 1 CYS B 136 ? ? -166.21 115.53 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LEU 8 ? CG ? A LEU 8 CG 2 1 Y 1 A LEU 8 ? CD1 ? A LEU 8 CD1 3 1 Y 1 A LEU 8 ? CD2 ? A LEU 8 CD2 4 1 Y 1 B HIS 135 ? CG ? B HIS 35 CG 5 1 Y 1 B HIS 135 ? ND1 ? B HIS 35 ND1 6 1 Y 1 B HIS 135 ? CD2 ? B HIS 35 CD2 7 1 Y 1 B HIS 135 ? CE1 ? B HIS 35 CE1 8 1 Y 1 B HIS 135 ? NE2 ? B HIS 35 NE2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLU 1 ? A GLU 1 2 1 Y 1 A ALA 2 ? A ALA 2 3 1 Y 1 A GLU 3 ? A GLU 3 4 1 Y 1 A GLU 4 ? A GLU 4 5 1 Y 1 A ASP 5 ? A ASP 5 6 1 Y 1 A GLY 6 ? A GLY 6 7 1 Y 1 A ASP 7 ? A ASP 7 8 1 Y 1 A SER 70 ? A SER 70 9 1 Y 1 B GLU 101 ? B GLU 1 10 1 Y 1 B ALA 102 ? B ALA 2 11 1 Y 1 B GLU 103 ? B GLU 3 12 1 Y 1 B GLU 104 ? B GLU 4 13 1 Y 1 B ASP 105 ? B ASP 5 14 1 Y 1 B GLY 106 ? B GLY 6 # 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 ZDO 1 C ZDO 1 F FDX 5 n C 2 IDS 2 C IDS 2 F FDX 5 n C 2 SUS 3 C SUS 3 F FDX 5 n C 2 BDP 4 C BDP 4 F FDX 5 n C 2 SGN 5 C SGN 5 F FDX 5 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 BDP 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpAb BDP 'COMMON NAME' GMML 1.0 'b-D-glucopyranuronic acid' BDP 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpA BDP 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcA IDS 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-L-IdopA2SO3 SGN 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 'DGlcpNS[6S]a' SGN 'COMMON NAME' GMML 1.0 N-sulfo-6-sulfo-a-D-glucopyranose SGN 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-GlcpNSO36SO3 SUS 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-GlcpNSO33SO36SO3 # _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=2.0/5,5,4/[a2122h-1a_1-5_1*OC_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-3-4-5/a4-b1_b4-c1_c4-d1_d4-e1 ; WURCS PDB2Glycan 1.1.0 2 2 ;[][methyl]{[(1+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO33SO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}}} ; LINUCS PDB-CARE ? # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.value_order _pdbx_entity_branch_link.details 1 2 2 IDS C1 O1 1 ZDO O4 HO4 sing ? 2 2 3 SUS C1 O1 2 IDS O4 HO4 sing ? 3 2 4 BDP C1 O1 3 SUS O4 HO4 sing ? 4 2 5 SGN C1 O1 4 BDP O4 HO4 sing ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 2 ZDO 1 n 2 IDS 2 n 2 SUS 3 n 2 BDP 4 n 2 SGN 5 n # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #