data_3HB9 # _model_server_result.job_id YMRb74gQT4N6KlottYTUlw _model_server_result.datetime_utc '2024-11-15 05:40:47' _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 3hb9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2100}' # _entry.id 3HB9 # _exptl.entry_id 3HB9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 109.65 _cell.angle_gamma 90 _cell.entry_id 3HB9 _cell.length_a 96.566 _cell.length_b 256.763 _cell.length_c 126.485 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HB9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 3 F N N ? 3 K 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 A NZ LYS 1112 A LYS 1144 1_555 E C11 BTI . A BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 B NZ LYS 1112 B LYS 1144 1_555 H C11 BTI . B BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 C NZ LYS 1112 C LYS 1144 1_555 J C11 BTI . C BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 C OD1 ASP 542 C ASP 572 1_555 L MN MN . C MN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc2 D OD1 ASP 542 D ASP 572 1_555 N MN MN . D MN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3HB9 _atom_sites.fract_transf_matrix[1][1] 0.010356 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003697 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003895 _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] 0.008395 _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 E 2 BTI A 1 2000 2000 BTI BTI . F 3 ADP A 1 2100 2100 ADP ADP . G 4 MN A 1 2002 2002 MN MN . H 2 BTI B 1 2000 2000 BTI BTI . I 4 MN B 1 2002 2002 MN MN . J 2 BTI C 1 2000 2000 BTI BTI . K 3 ADP C 1 2100 2100 ADP ADP . L 4 MN C 1 2002 2002 MN MN . M 2 BTI C 1 1183 2000 BTI BTI . N 4 MN D 1 2002 2002 MN MN . # 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 P PB ADP . . . F 3 87.758 47.406 1.661 1 103.29 ? PB ADP 2100 A 1 HETATM 2 O O1B ADP . . . F 3 87.727 45.99 2.186 1 103.21 ? O1B ADP 2100 A 1 HETATM 3 O O2B ADP . . . F 3 88.368 48.402 2.619 1 103.26 ? O2B ADP 2100 A 1 HETATM 4 O O3B ADP . . . F 3 86.473 47.873 1.018 1 103.17 ? O3B ADP 2100 A 1 HETATM 5 P PA ADP . . . F 3 88.7 46.224 -0.717 1 103.17 ? PA ADP 2100 A 1 HETATM 6 O O1A ADP . . . F 3 87.24 45.992 -1.04 1 103.21 ? O1A ADP 2100 A 1 HETATM 7 O O2A ADP . . . F 3 89.575 45.056 -0.328 1 102.99 ? O2A ADP 2100 A 1 HETATM 8 O O3A ADP . . . F 3 88.809 47.345 0.44 1 103.16 ? O3A ADP 2100 A 1 HETATM 9 O O5' ADP . . . F 3 89.389 46.954 -1.979 1 102.55 ? O5' ADP 2100 A 1 HETATM 10 C C5' ADP . . . F 3 88.795 48.115 -2.559 1 101.53 ? C5' ADP 2100 A 1 HETATM 11 C C4' ADP . . . F 3 89.597 48.595 -3.761 1 100.69 ? C4' ADP 2100 A 1 HETATM 12 O O4' ADP . . . F 3 90.999 48.398 -3.556 1 100.32 ? O4' ADP 2100 A 1 HETATM 13 C C3' ADP . . . F 3 89.23 47.837 -5.026 1 100.41 ? C3' ADP 2100 A 1 HETATM 14 O O3' ADP . . . F 3 88.234 48.532 -5.781 1 100.51 ? O3' ADP 2100 A 1 HETATM 15 C C2' ADP . . . F 3 90.526 47.736 -5.799 1 100.27 ? C2' ADP 2100 A 1 HETATM 16 O O2' ADP . . . F 3 90.619 48.764 -6.792 1 100.13 ? O2' ADP 2100 A 1 HETATM 17 C C1' ADP . . . F 3 91.62 47.923 -4.758 1 100.12 ? C1' ADP 2100 A 1 HETATM 18 N N9 ADP . . . F 3 92.314 46.623 -4.538 1 100.02 ? N9 ADP 2100 A 1 HETATM 19 C C8 ADP . . . F 3 92.28 45.878 -3.415 1 99.97 ? C8 ADP 2100 A 1 HETATM 20 N N7 ADP . . . F 3 93.025 44.749 -3.547 1 100.02 ? N7 ADP 2100 A 1 HETATM 21 C C5 ADP . . . F 3 93.555 44.757 -4.785 1 100.03 ? C5 ADP 2100 A 1 HETATM 22 C C6 ADP . . . F 3 94.442 43.87 -5.583 1 100 ? C6 ADP 2100 A 1 HETATM 23 N N6 ADP . . . F 3 94.922 42.713 -5.067 1 100.03 ? N6 ADP 2100 A 1 HETATM 24 N N1 ADP . . . F 3 94.756 44.252 -6.844 1 99.94 ? N1 ADP 2100 A 1 HETATM 25 C C2 ADP . . . F 3 94.285 45.399 -7.374 1 99.95 ? C2 ADP 2100 A 1 HETATM 26 N N3 ADP . . . F 3 93.482 46.249 -6.709 1 99.94 ? N3 ADP 2100 A 1 HETATM 27 C C4 ADP . . . F 3 93.086 45.994 -5.434 1 99.97 ? C4 ADP 2100 A 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 385 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #