data_5VDW # _model_server_result.job_id TFyAV-QRElYmH-Kjajis5w _model_server_result.datetime_utc '2024-10-15 12:21:59' _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 5vdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":602}' # _entry.id 5VDW # _exptl.entry_id 5VDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 259.284 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[2-(1,3-thiazol-4-yl)-1H-benzimidazol-1-yl]acetic acid' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.29 _cell.angle_gamma 90 _cell.entry_id 5VDW _cell.length_a 217.36 _cell.length_b 47.998 _cell.length_c 86.861 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VDW _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 NE2 HIS 231 A HIS 390 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc2 A SG CYS 237 A CYS 396 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc3 A SG CYS 238 A CYS 397 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc4 A SG CYS 245 A CYS 404 1_555 C ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc5 B NE2 HIS 231 B HIS 390 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc6 B SG CYS 237 B CYS 396 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc7 B SG CYS 238 B CYS 397 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc8 B SG CYS 245 B CYS 404 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? # _chem_comp.formula 'C12 H9 N3 O2 S' _chem_comp.formula_weight 259.284 _chem_comp.id 9BY _chem_comp.mon_nstd_flag . _chem_comp.name '[2-(1,3-thiazol-4-yl)-1H-benzimidazol-1-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 S1 C11 9BY sing 1 n y S1 C12 9BY sing 2 n y C11 C10 9BY doub 3 n y C12 N3 9BY doub 4 n y C10 N3 9BY sing 5 n y C10 C7 9BY sing 6 n n N1 C7 9BY doub 7 n y N1 C5 9BY sing 8 n y C7 N2 9BY sing 9 n y C5 C6 9BY doub 10 n y C5 C4 9BY sing 11 n y N2 C8 9BY sing 12 n n N2 C4 9BY sing 13 n y C6 C1 9BY sing 14 n y O2 C9 9BY doub 15 n n C8 C9 9BY sing 16 n n C4 C3 9BY doub 17 n y C9 O1 9BY sing 18 n n C1 C2 9BY doub 19 n y C3 C2 9BY sing 20 n y C6 H1 9BY sing 21 n n C8 H2 9BY sing 22 n n C8 H3 9BY sing 23 n n C1 H4 9BY sing 24 n n C2 H5 9BY sing 25 n n C3 H6 9BY sing 26 n n O1 H7 9BY sing 27 n n C11 H8 9BY sing 28 n n C12 H9 9BY sing 29 n n # _atom_sites.entry_id 5VDW _atom_sites.fract_transf_matrix[1][1] 0.004601 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001258 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020834 _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] 0.011935 _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 2 ZN A 1 601 601 ZN ZN . D 3 9BY A 1 602 1 9BY PFE . E 2 ZN B 1 601 601 ZN ZN . F 3 9BY B 1 602 1 9BY PFE . G 4 HOH A 1 701 33 HOH HOH . G 4 HOH A 2 702 12 HOH HOH . G 4 HOH A 3 703 35 HOH HOH . G 4 HOH A 4 704 16 HOH HOH . G 4 HOH A 5 705 9 HOH HOH . G 4 HOH A 6 706 5 HOH HOH . G 4 HOH A 7 707 10 HOH HOH . G 4 HOH A 8 708 17 HOH HOH . G 4 HOH A 9 709 11 HOH HOH . G 4 HOH A 10 710 27 HOH HOH . G 4 HOH A 11 711 31 HOH HOH . G 4 HOH A 12 712 7 HOH HOH . G 4 HOH A 13 713 20 HOH HOH . G 4 HOH A 14 714 3 HOH HOH . G 4 HOH A 15 715 34 HOH HOH . G 4 HOH A 16 716 4 HOH HOH . G 4 HOH A 17 717 36 HOH HOH . G 4 HOH A 18 718 8 HOH HOH . G 4 HOH A 19 719 26 HOH HOH . G 4 HOH A 20 720 19 HOH HOH . G 4 HOH A 21 721 21 HOH HOH . H 4 HOH B 1 701 23 HOH HOH . H 4 HOH B 2 702 1 HOH HOH . H 4 HOH B 3 703 22 HOH HOH . H 4 HOH B 4 704 32 HOH HOH . H 4 HOH B 5 705 6 HOH HOH . H 4 HOH B 6 706 15 HOH HOH . H 4 HOH B 7 707 14 HOH HOH . H 4 HOH B 8 708 29 HOH HOH . H 4 HOH B 9 709 18 HOH HOH . H 4 HOH B 10 710 24 HOH HOH . H 4 HOH B 11 711 2 HOH HOH . H 4 HOH B 12 712 28 HOH HOH . H 4 HOH B 13 713 13 HOH HOH . H 4 HOH B 14 714 30 HOH HOH . H 4 HOH B 15 715 25 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 N N3 9BY . . . F 3 -27.998 0.939 23.043 1 108.7 ? N3 9BY 602 B 1 HETATM 2 C C4 9BY . . . F 3 -27.433 -2.96 21.068 1 86.67 ? C4 9BY 602 B 1 HETATM 3 N N2 9BY . . . F 3 -27.553 -1.611 21.382 1 91.69 ? N2 9BY 602 B 1 HETATM 4 C C7 9BY . . . F 3 -27.921 -1.556 22.71 1 95.55 ? C7 9BY 602 B 1 HETATM 5 C C6 9BY . . . F 3 -27.703 -5.034 22.258 1 80.28 ? C6 9BY 602 B 1 HETATM 6 C C9 9BY . . . F 3 -25.847 -0.253 20.296 1 95.2 ? C9 9BY 602 B 1 HETATM 7 C C8 9BY . . . F 3 -27.327 -0.515 20.447 1 92.21 ? C8 9BY 602 B 1 HETATM 8 C C1 9BY . . . F 3 -27.354 -5.703 21.094 1 78.49 ? C1 9BY 602 B 1 HETATM 9 C C2 9BY . . . F 3 -27.049 -5.004 19.93 1 80.1 ? C2 9BY 602 B 1 HETATM 10 C C3 9BY . . . F 3 -27.085 -3.618 19.9 1 82.42 ? C3 9BY 602 B 1 HETATM 11 C C5 9BY . . . F 3 -27.741 -3.643 22.239 1 85.57 ? C5 9BY 602 B 1 HETATM 12 N N1 9BY . . . F 3 -28.048 -2.746 23.262 1 90.71 ? N1 9BY 602 B 1 HETATM 13 O O1 9BY . . . F 3 -25.227 -0.11 21.438 1 98.27 ? O1 9BY 602 B 1 HETATM 14 O O2 9BY . . . F 3 -25.297 -0.184 19.217 1 95.01 ? O2 9BY 602 B 1 HETATM 15 C C10 9BY . . . F 3 -28.149 -0.355 23.525 1 103.22 ? C10 9BY 602 B 1 HETATM 16 C C11 9BY . . . F 3 -28.516 -0.431 24.83 1 104.83 ? C11 9BY 602 B 1 HETATM 17 S S1 9BY . . . F 3 -28.689 1.116 25.522 1 110.05 ? S1 9BY 602 B 1 HETATM 18 C C12 9BY . . . F 3 -28.252 1.785 23.991 1 110.77 ? C12 9BY 602 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 18 #