data_6QP0 # _model_server_result.job_id OXCBwP35KussrqFiOxGUmA _model_server_result.datetime_utc '2024-10-19 21:43:08' _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 6qp0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6QP0 # _exptl.entry_id 6QP0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 6QP0 _cell.length_a 71.02 _cell.length_b 71.02 _cell.length_c 88.57 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QP0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 OG1 THR 16 A THR 15 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc2 A OD1 ASP 130 A ASP 129 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc3 B O1B ADP . A ADP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc4 D MG MG . A MG 503 1_555 F O HOH . A HOH 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? # _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 ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6QP0 _atom_sites.fract_transf_matrix[1][1] 0.014081 _atom_sites.fract_transf_matrix[1][2] 0.008129 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016259 _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] 0.011291 _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 B 2 ADP A 1 501 501 ADP ADP . C 3 AF3 A 1 502 601 AF3 AF3 . D 4 MG A 1 503 701 MG MG . E 5 MES A 1 504 801 MES MES . F 6 HOH A 1 901 16 HOH HOH . F 6 HOH A 2 902 21 HOH HOH . F 6 HOH A 3 903 19 HOH HOH . F 6 HOH A 4 904 48 HOH HOH . F 6 HOH A 5 905 32 HOH HOH . F 6 HOH A 6 906 35 HOH HOH . F 6 HOH A 7 907 1 HOH HOH . F 6 HOH A 8 908 27 HOH HOH . F 6 HOH A 9 909 5 HOH HOH . F 6 HOH A 10 910 8 HOH HOH . F 6 HOH A 11 911 39 HOH HOH . F 6 HOH A 12 912 43 HOH HOH . F 6 HOH A 13 913 28 HOH HOH . F 6 HOH A 14 914 3 HOH HOH . F 6 HOH A 15 915 4 HOH HOH . F 6 HOH A 16 916 51 HOH HOH . F 6 HOH A 17 917 30 HOH HOH . F 6 HOH A 18 918 29 HOH HOH . F 6 HOH A 19 919 13 HOH HOH . F 6 HOH A 20 920 14 HOH HOH . F 6 HOH A 21 921 15 HOH HOH . F 6 HOH A 22 922 36 HOH HOH . F 6 HOH A 23 923 20 HOH HOH . F 6 HOH A 24 924 45 HOH HOH . F 6 HOH A 25 925 23 HOH HOH . F 6 HOH A 26 926 10 HOH HOH . F 6 HOH A 27 927 40 HOH HOH . F 6 HOH A 28 928 17 HOH HOH . F 6 HOH A 29 929 2 HOH HOH . F 6 HOH A 30 930 6 HOH HOH . F 6 HOH A 31 931 7 HOH HOH . F 6 HOH A 32 932 46 HOH HOH . F 6 HOH A 33 933 52 HOH HOH . F 6 HOH A 34 934 18 HOH HOH . F 6 HOH A 35 935 9 HOH HOH . F 6 HOH A 36 936 12 HOH HOH . F 6 HOH A 37 937 49 HOH HOH . F 6 HOH A 38 938 34 HOH HOH . F 6 HOH A 39 939 11 HOH HOH . F 6 HOH A 40 940 53 HOH HOH . F 6 HOH A 41 941 47 HOH HOH . F 6 HOH A 42 942 38 HOH HOH . F 6 HOH A 43 943 44 HOH HOH . F 6 HOH A 44 944 31 HOH HOH . F 6 HOH A 45 945 42 HOH HOH . F 6 HOH A 46 946 24 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 P PB ADP . . . B 2 -4.635 26.322 42.357 1 49.73 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . B 2 -5.459 26.507 41.102 1 53.57 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . B 2 -3.322 25.677 42.013 1 44.27 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . B 2 -4.371 27.661 43.002 1 50.31 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . B 2 -7.053 25.034 43.403 1 53.81 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . B 2 -7.427 24.392 42.089 1 53.53 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . B 2 -7.824 26.322 43.591 1 51.69 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . B 2 -5.429 25.335 43.423 1 52.03 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . B 2 -7.385 23.975 44.638 1 58.74 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . B 2 -6.525 22.864 44.798 1 62.95 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . B 2 -7.176 21.828 45.466 1 65.93 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . B 2 -7.237 22.119 46.946 1 67.97 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . B 2 -8.7 21.7 44.985 1 66.91 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . B 2 -9.112 20.257 44.96 1 67.29 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . B 2 -9.364 22.321 45.826 1 68.38 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . B 2 -10.663 21.64 46.035 1 68.14 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . B 2 -8.491 22.322 47.24 1 70.52 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . B 2 -8.624 23.596 47.861 1 72.94 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . B 2 -8.254 24.822 47.494 1 75.14 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . B 2 -8.639 25.655 48.467 1 75.21 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . B 2 -9.242 24.928 49.423 1 75.25 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . B 2 -9.816 25.283 50.625 1 74.05 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . B 2 -10.169 26.318 51.591 1 75.64 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . B 2 -10.356 24.363 51.405 1 74.69 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . B 2 -10.348 23.064 51.024 1 77.1 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . B 2 -9.787 22.706 49.844 1 76.51 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . B 2 -9.236 23.645 49.05 1 75.76 ? C4 ADP 501 A 1 HETATM 28 H "H5'1" ADP . . . B 2 -5.747 23.134 45.311 1 75.54 ? "H5'1" ADP 501 A 1 HETATM 29 H "H5'2" ADP . . . B 2 -6.242 22.551 43.924 1 75.54 ? "H5'2" ADP 501 A 1 HETATM 30 H H4' ADP . . . B 2 -6.716 20.988 45.308 1 79.13 ? H4' ADP 501 A 1 HETATM 31 H H3' ADP . . . B 2 -8.811 22.101 44.109 1 80.3 ? H3' ADP 501 A 1 HETATM 32 H H2' ADP . . . B 2 -9.487 23.236 45.528 1 82.06 ? H2' ADP 501 A 1 HETATM 33 H HO2' ADP . . . B 2 -11.282 22.091 45.665 1 81.77 ? HO2' ADP 501 A 1 HETATM 34 H H1' ADP . . . B 2 -8.801 21.596 47.804 1 84.64 ? H1' ADP 501 A 1 HETATM 35 H H8 ADP . . . B 2 -7.811 25.055 46.709 1 90.17 ? H8 ADP 501 A 1 HETATM 36 H HN61 ADP . . . B 2 -10.178 26.136 52.432 1 90.78 ? HN61 ADP 501 A 1 HETATM 37 H HN62 ADP . . . B 2 -10.368 27.109 51.32 1 90.78 ? HN62 ADP 501 A 1 HETATM 38 H H2 ADP . . . B 2 -10.727 22.416 51.573 1 92.53 ? H2 ADP 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 38 #