data_5GTD # _model_server_result.job_id 5KVGE7WoNdPHlbAqe5_BWA _model_server_result.datetime_utc '2024-12-24 17:36:26' _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":"K","auth_seq_id":503}' # _entry.id 5GTD # _exptl.entry_id 5GTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 69.085 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description IMIDAZOLE _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 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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id K _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 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 'C3 H5 N2 1' _chem_comp.formula_weight 69.085 _chem_comp.id IMD _chem_comp.mon_nstd_flag . _chem_comp.name IMIDAZOLE _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 N1 C2 IMD sing 212 n y N1 C5 IMD sing 213 n y N1 HN1 IMD sing 214 n n C2 N3 IMD doub 215 n y C2 H2 IMD sing 216 n n N3 C4 IMD sing 217 n y N3 HN3 IMD sing 218 n n C4 C5 IMD doub 219 n y C4 H4 IMD sing 220 n n C5 H5 IMD sing 221 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 N N1 IMD . . . K 7 44.601 -137.687 -6.98 1 103.7 ? N1 IMD 503 B 1 HETATM 2 C C2 IMD . . . K 7 45.898 -137.436 -6.674 1 104.79 ? C2 IMD 503 B 1 HETATM 3 N N3 IMD . . . K 7 45.932 -136.809 -5.472 1 104.98 1 N3 IMD 503 B 1 HETATM 4 C C4 IMD . . . K 7 44.675 -136.675 -5.04 1 106.24 ? C4 IMD 503 B 1 HETATM 5 C C5 IMD . . . K 7 43.844 -137.223 -5.981 1 105.76 ? C5 IMD 503 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 5 #