data_5GTD # _model_server_result.job_id QYCoh0RZhj9mikU7OIZhKQ _model_server_result.datetime_utc '2024-12-24 17:47:00' _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 5gtd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":506}' # _entry.id 5GTD # _exptl.entry_id 5GTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 222.194 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-SUCCINYLBENZOATE _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 90 _cell.angle_gamma 90 _cell.entry_id 5GTD _cell.length_a 121.814 _cell.length_b 121.814 _cell.length_c 98.563 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GTD _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43' # _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,H,I,J,K,L,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 H N N ? 5 M 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 covale ? covale1 G P AMP . A AMP 505 1_555 H O5 OSB . A OSB 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? covale ? covale2 L P AMP . B AMP 504 1_555 M O4 OSB . B OSB 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? metalc ? metalc1 B O PRO 8 B PRO 6 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc2 B OE1 GLN 13 B GLN 11 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? # _chem_comp.formula 'C11 H10 O5' _chem_comp.formula_weight 222.194 _chem_comp.id OSB _chem_comp.mon_nstd_flag . _chem_comp.name 2-SUCCINYLBENZOATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms O-SUCCINYLBENZOATE # 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 O1 C7 OSB sing 286 n n O1 HO1 OSB sing 287 n n O2 C7 OSB doub 288 n n C7 C2 OSB sing 289 n n C6 C5 OSB doub 290 n y C6 C1 OSB sing 291 n y C6 H61 OSB sing 292 n n C5 C4 OSB sing 293 n y C5 H51 OSB sing 294 n n C4 C3 OSB doub 295 n y C4 H41 OSB sing 296 n n C3 C2 OSB sing 297 n y C3 H31 OSB sing 298 n n C2 C1 OSB doub 299 n y C1 C8 OSB sing 300 n n C8 C9 OSB sing 301 n n C8 O3 OSB doub 302 n n C9 C10 OSB sing 303 n n C9 H91 OSB sing 304 n n C9 H92 OSB sing 305 n n C10 C11 OSB sing 306 n n C10 H101 OSB sing 307 n n C10 H102 OSB sing 308 n n C11 O4 OSB doub 309 n n C11 O5 OSB sing 310 n n O5 HO5 OSB sing 311 n n # _atom_sites.entry_id 5GTD _atom_sites.fract_transf_matrix[1][1] 0.008209 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008209 _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] 0.010146 _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 CL A 1 501 2 CL CL . D 2 CL A 1 502 5 CL CL . E 2 CL A 1 503 6 CL CL . F 3 PEG A 1 504 1 PEG PEG . G 4 AMP A 1 505 500 AMP DRG . H 5 OSB A 1 506 500 OSB DRG . I 2 CL B 1 501 3 CL CL . J 6 MG B 1 502 2 MG MG . K 7 IMD B 1 503 1 IMD IMD . L 4 AMP B 1 504 500 AMP DRG . M 5 OSB B 1 505 500 OSB DRG . N 8 HOH A 1 601 18 HOH HOH . N 8 HOH A 2 602 17 HOH HOH . N 8 HOH A 3 603 11 HOH HOH . N 8 HOH A 4 604 7 HOH HOH . N 8 HOH A 5 605 8 HOH HOH . N 8 HOH A 6 606 36 HOH HOH . N 8 HOH A 7 607 10 HOH HOH . N 8 HOH A 8 608 6 HOH HOH . N 8 HOH A 9 609 12 HOH HOH . N 8 HOH A 10 610 51 HOH HOH . N 8 HOH A 11 611 22 HOH HOH . N 8 HOH A 12 612 20 HOH HOH . N 8 HOH A 13 613 14 HOH HOH . N 8 HOH A 14 614 43 HOH HOH . N 8 HOH A 15 615 47 HOH HOH . N 8 HOH A 16 616 40 HOH HOH . N 8 HOH A 17 617 25 HOH HOH . N 8 HOH A 18 618 48 HOH HOH . N 8 HOH A 19 619 53 HOH HOH . N 8 HOH A 20 620 54 HOH HOH . N 8 HOH A 21 621 33 HOH HOH . N 8 HOH A 22 622 1 HOH HOH . N 8 HOH A 23 623 35 HOH HOH . N 8 HOH A 24 624 49 HOH HOH . N 8 HOH A 25 625 9 HOH HOH . N 8 HOH A 26 626 38 HOH HOH . N 8 HOH A 27 627 13 HOH HOH . O 8 HOH B 1 601 28 HOH HOH . O 8 HOH B 2 602 21 HOH HOH . O 8 HOH B 3 603 2 HOH HOH . O 8 HOH B 4 604 39 HOH HOH . O 8 HOH B 5 605 3 HOH HOH . O 8 HOH B 6 606 44 HOH HOH . O 8 HOH B 7 607 5 HOH HOH . O 8 HOH B 8 608 4 HOH HOH . O 8 HOH B 9 609 50 HOH HOH . O 8 HOH B 10 610 24 HOH HOH . O 8 HOH B 11 611 46 HOH HOH . O 8 HOH B 12 612 15 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 O O1 OSB . . . H 5 52.353 -152.852 -5.752 1 73.65 ? O1 OSB 506 A 1 HETATM 2 O O2 OSB . . . H 5 53.963 -151.981 -6.927 1 80.89 ? O2 OSB 506 A 1 HETATM 3 C C7 OSB . . . H 5 53.065 -152.847 -6.786 1 75.62 ? C7 OSB 506 A 1 HETATM 4 C C6 OSB . . . H 5 53.71 -155.642 -9.218 1 81.64 ? C6 OSB 506 A 1 HETATM 5 C C5 OSB . . . H 5 52.443 -155.773 -9.814 1 76.12 ? C5 OSB 506 A 1 HETATM 6 C C4 OSB . . . H 5 51.388 -154.943 -9.412 1 66.72 ? C4 OSB 506 A 1 HETATM 7 C C3 OSB . . . H 5 51.591 -153.996 -8.431 1 63.69 ? C3 OSB 506 A 1 HETATM 8 C C2 OSB . . . H 5 52.846 -153.864 -7.839 1 73.41 ? C2 OSB 506 A 1 HETATM 9 C C1 OSB . . . H 5 53.912 -154.703 -8.246 1 80.73 ? C1 OSB 506 A 1 HETATM 10 C C8 OSB . . . H 5 55.291 -154.558 -7.596 1 80.56 ? C8 OSB 506 A 1 HETATM 11 C C9 OSB . . . H 5 56.571 -154.806 -8.431 1 89.7 ? C9 OSB 506 A 1 HETATM 12 O O3 OSB . . . H 5 55.38 -154.248 -6.42 1 78.46 ? O3 OSB 506 A 1 HETATM 13 C C10 OSB . . . H 5 57.774 -154.88 -7.507 1 92.84 ? C10 OSB 506 A 1 HETATM 14 C C11 OSB . . . H 5 58.676 -156.012 -7.943 1 100.06 ? C11 OSB 506 A 1 HETATM 15 O O4 OSB . . . H 5 58.657 -156.393 -9.097 1 105.56 ? O4 OSB 506 A 1 HETATM 16 O O5 OSB . . . H 5 59.544 -156.631 -7.006 1 101.76 ? O5 OSB 506 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 16 #