data_5HBM # _model_server_result.job_id bUfsu4Hc8y_yGzAS3lzD1g _model_server_result.datetime_utc '2024-10-19 06:38:01' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5hbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 5HBM # _exptl.entry_id 5HBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 236.178 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(7,8-dihydroxy-2-oxo-2H-chromen-4-yl)acetic acid' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.62 _cell.angle_gamma 90 _cell.entry_id 5HBM _cell.length_a 103.931 _cell.length_b 69.472 _cell.length_c 219.344 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD2 ASP 445 A ASP 443 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc2 A OD1 ASP 445 A ASP 443 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc3 A OE2 GLU 480 A GLU 478 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc4 A OD1 ASP 500 A ASP 498 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc5 A OD2 ASP 500 A ASP 498 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc6 A OD1 ASP 551 A ASP 549 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc7 D O1 F95 . A F95 602 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc8 D O2 F95 . A F95 602 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc9 D O1 F95 . A F95 602 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc10 D O3 F95 . A F95 602 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc11 E MN MN . A MN 603 1_555 G O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? # _chem_comp.formula 'C11 H8 O6' _chem_comp.formula_weight 236.178 _chem_comp.id F95 _chem_comp.mon_nstd_flag . _chem_comp.name '(7,8-dihydroxy-2-oxo-2H-chromen-4-yl)acetic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O4 C7 F95 doub 83 n n C7 C8 F95 sing 84 n n C7 O3 F95 sing 85 n n C8 C9 F95 doub 86 n n C9 C10 F95 sing 87 n n C9 C1 F95 sing 88 n n C10 C11 F95 sing 89 n n O3 C2 F95 sing 90 n n C1 C2 F95 doub 91 n y C1 C6 F95 sing 92 n y C2 C3 F95 sing 93 n y C6 C5 F95 doub 94 n y C3 O1 F95 sing 95 n n C3 C4 F95 doub 96 n y C5 C4 F95 sing 97 n y C4 O2 F95 sing 98 n n O6 C11 F95 doub 99 n n C11 O5 F95 sing 100 n n C5 H1 F95 sing 101 n n C6 H2 F95 sing 102 n n O1 H3 F95 sing 103 n n O2 H4 F95 sing 104 n n C8 H5 F95 sing 105 n n C10 H6 F95 sing 106 n n C10 H7 F95 sing 107 n n O5 H8 F95 sing 108 n n # _atom_sites.entry_id 5HBM _atom_sites.fract_transf_matrix[1][1] 0.009622 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001803 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014394 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004638 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code C 3 NVP A 1 601 560 NVP NVP . D 4 F95 A 1 602 561 F95 F95 . E 5 MN A 1 603 562 MN MN . F 5 MN A 1 604 563 MN MN . G 6 HOH A 1 701 564 HOH HOH . G 6 HOH A 2 702 565 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 F95 . . . D 4 -27.921 -4.801 228.579 1 93.44 ? C1 F95 602 A 1 HETATM 2 C C2 F95 . . . D 4 -28.456 -5.858 227.761 1 85.02 ? C2 F95 602 A 1 HETATM 3 C C3 F95 . . . D 4 -29.496 -5.589 226.89 1 84.74 ? C3 F95 602 A 1 HETATM 4 C C4 F95 . . . D 4 -30.017 -4.301 226.809 1 90.55 ? C4 F95 602 A 1 HETATM 5 C C5 F95 . . . D 4 -29.496 -3.279 227.603 1 90.06 ? C5 F95 602 A 1 HETATM 6 C C6 F95 . . . D 4 -28.454 -3.531 228.484 1 93.26 ? C6 F95 602 A 1 HETATM 7 O O1 F95 . . . D 4 -30.025 -6.616 226.088 1 81.52 ? O1 F95 602 A 1 HETATM 8 O O2 F95 . . . D 4 -31.077 -4.036 225.92 1 82.26 ? O2 F95 602 A 1 HETATM 9 O O3 F95 . . . D 4 -27.92 -7.154 227.853 1 78.98 ? O3 F95 602 A 1 HETATM 10 C C7 F95 . . . D 4 -26.908 -7.418 228.7 1 79.82 ? C7 F95 602 A 1 HETATM 11 C C8 F95 . . . D 4 -26.334 -6.388 229.545 1 97.23 ? C8 F95 602 A 1 HETATM 12 C C9 F95 . . . D 4 -26.831 -5.102 229.484 1 96.12 ? C9 F95 602 A 1 HETATM 13 O O4 F95 . . . D 4 -26.402 -8.722 228.768 1 74.87 ? O4 F95 602 A 1 HETATM 14 C C10 F95 . . . D 4 -26.235 -4.026 230.371 1 97.76 ? C10 F95 602 A 1 HETATM 15 C C11 F95 . . . D 4 -25.428 -3.046 229.549 1 104.42 ? C11 F95 602 A 1 HETATM 16 O O5 F95 . . . D 4 -25.516 -1.814 229.793 1 121.91 -1 O5 F95 602 A 1 HETATM 17 O O6 F95 . . . D 4 -24.678 -3.462 228.627 1 92.69 ? O6 F95 602 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 17 #