data_1XW4 # _model_server_result.job_id 8ZKahIQxvNCc8gs-czqjeA _model_server_result.datetime_utc '2025-01-27 04:32:18' _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 1xw4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":998}' # _entry.id 1XW4 # _exptl.entry_id 1XW4 _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 1XW4 _cell.length_a 68.451 _cell.length_b 68.451 _cell.length_c 50.891 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XW4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 covale ? covale1 A C GLY 71 X GLY 98 1_555 A N CSD 72 X CSD 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C CSD 72 X CSD 99 1_555 A N HIS 73 X HIS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _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 1XW4 _atom_sites.fract_transf_matrix[1][1] 0.014609 _atom_sites.fract_transf_matrix[1][2] 0.008435 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016869 _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] 0.01965 _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 X 1 998 998 ADP ADP . C 3 HOH X 1 999 1 HOH HOH . C 3 HOH X 2 1000 2 HOH HOH . C 3 HOH X 3 1001 3 HOH HOH . C 3 HOH X 4 1002 4 HOH HOH . C 3 HOH X 5 1003 5 HOH HOH . C 3 HOH X 6 1004 6 HOH HOH . C 3 HOH X 7 1005 7 HOH HOH . C 3 HOH X 8 1006 8 HOH HOH . C 3 HOH X 9 1007 9 HOH HOH . C 3 HOH X 10 1008 10 HOH HOH . C 3 HOH X 11 1009 11 HOH HOH . C 3 HOH X 12 1010 12 HOH HOH . C 3 HOH X 13 1011 13 HOH HOH . C 3 HOH X 14 1012 14 HOH HOH . C 3 HOH X 15 1013 15 HOH HOH . C 3 HOH X 16 1014 16 HOH HOH . C 3 HOH X 17 1015 17 HOH HOH . C 3 HOH X 18 1016 18 HOH HOH . C 3 HOH X 19 1017 19 HOH HOH . C 3 HOH X 20 1018 20 HOH HOH . C 3 HOH X 21 1019 21 HOH HOH . C 3 HOH X 22 1020 22 HOH HOH . C 3 HOH X 23 1021 23 HOH HOH . C 3 HOH X 24 1022 24 HOH HOH . C 3 HOH X 25 1023 25 HOH HOH . C 3 HOH X 26 1024 26 HOH HOH . C 3 HOH X 27 1025 27 HOH HOH . C 3 HOH X 28 1026 28 HOH HOH . C 3 HOH X 29 1027 29 HOH HOH . C 3 HOH X 30 1028 30 HOH HOH . C 3 HOH X 31 1029 31 HOH HOH . C 3 HOH X 32 1030 32 HOH HOH . C 3 HOH X 33 1031 33 HOH HOH . C 3 HOH X 34 1032 34 HOH HOH . C 3 HOH X 35 1033 35 HOH HOH . C 3 HOH X 36 1034 36 HOH HOH . C 3 HOH X 37 1035 37 HOH HOH . C 3 HOH X 38 1036 38 HOH HOH . C 3 HOH X 39 1037 39 HOH HOH . C 3 HOH X 40 1038 40 HOH HOH . C 3 HOH X 41 1039 41 HOH HOH . C 3 HOH X 42 1040 42 HOH HOH . C 3 HOH X 43 1041 43 HOH HOH . C 3 HOH X 44 1042 44 HOH HOH . C 3 HOH X 45 1043 45 HOH HOH . C 3 HOH X 46 1044 46 HOH HOH . C 3 HOH X 47 1045 47 HOH HOH . C 3 HOH X 48 1046 48 HOH HOH . C 3 HOH X 49 1047 49 HOH HOH . C 3 HOH X 50 1048 50 HOH HOH . C 3 HOH X 51 1049 51 HOH HOH . C 3 HOH X 52 1050 52 HOH HOH . C 3 HOH X 53 1051 53 HOH HOH . C 3 HOH X 54 1052 54 HOH HOH . C 3 HOH X 55 1053 55 HOH HOH . C 3 HOH X 56 1054 56 HOH HOH . C 3 HOH X 57 1055 57 HOH HOH . C 3 HOH X 58 1056 58 HOH HOH . C 3 HOH X 59 1057 59 HOH HOH . C 3 HOH X 60 1058 60 HOH HOH . C 3 HOH X 61 1059 61 HOH HOH . C 3 HOH X 62 1060 62 HOH HOH . C 3 HOH X 63 1061 63 HOH HOH . C 3 HOH X 64 1062 64 HOH HOH . C 3 HOH X 65 1063 65 HOH HOH . C 3 HOH X 66 1064 66 HOH HOH . C 3 HOH X 67 1065 67 HOH HOH . C 3 HOH X 68 1066 68 HOH HOH . C 3 HOH X 69 1067 69 HOH HOH . C 3 HOH X 70 1068 70 HOH HOH . C 3 HOH X 71 1069 71 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 32.596 -38.234 7.633 1 26.3 ? PB ADP 998 X 1 HETATM 2 O O1B ADP . . . B 2 33.357 -38.769 8.822 1 22.73 ? O1B ADP 998 X 1 HETATM 3 O O2B ADP . . . B 2 31.175 -37.765 7.947 1 22.69 ? O2B ADP 998 X 1 HETATM 4 O O3B ADP . . . B 2 33.305 -37.18 6.814 1 25.66 ? O3B ADP 998 X 1 HETATM 5 P PA ADP . . . B 2 32.737 -39.648 5.131 1 48.28 ? PA ADP 998 X 1 HETATM 6 O O1A ADP . . . B 2 32.595 -38.301 4.436 1 47.31 ? O1A ADP 998 X 1 HETATM 7 O O2A ADP . . . B 2 32.131 -40.925 4.54 1 50.2 ? O2A ADP 998 X 1 HETATM 8 O O3A ADP . . . B 2 32.269 -39.517 6.713 1 35.63 ? O3A ADP 998 X 1 HETATM 9 O O5' ADP . . . B 2 34.337 -39.959 5.201 1 47.56 ? O5' ADP 998 X 1 HETATM 10 C C5' ADP . . . B 2 34.863 -41.042 5.984 1 48.41 ? C5' ADP 998 X 1 HETATM 11 C C4' ADP . . . B 2 36.269 -41.353 5.481 1 50.06 ? C4' ADP 998 X 1 HETATM 12 O O4' ADP . . . B 2 36.666 -42.57 6.118 1 49.66 ? O4' ADP 998 X 1 HETATM 13 C C3' ADP . . . B 2 36.339 -41.615 3.969 1 51.22 ? C3' ADP 998 X 1 HETATM 14 O O3' ADP . . . B 2 37.521 -41.008 3.431 1 52.24 ? O3' ADP 998 X 1 HETATM 15 C C2' ADP . . . B 2 36.384 -43.135 3.819 1 51.48 ? C2' ADP 998 X 1 HETATM 16 O O2' ADP . . . B 2 37.185 -43.621 2.734 1 50.68 ? O2' ADP 998 X 1 HETATM 17 C C1' ADP . . . B 2 36.962 -43.594 5.15 1 51.9 ? C1' ADP 998 X 1 HETATM 18 N N9 ADP . . . B 2 36.358 -44.857 5.626 1 52.74 ? N9 ADP 998 X 1 HETATM 19 C C8 ADP . . . B 2 37.075 -45.9 6.083 1 52.68 ? C8 ADP 998 X 1 HETATM 20 N N7 ADP . . . B 2 36.244 -46.911 6.444 1 53.21 ? N7 ADP 998 X 1 HETATM 21 C C5 ADP . . . B 2 34.966 -46.51 6.237 1 52.88 ? C5 ADP 998 X 1 HETATM 22 C C6 ADP . . . B 2 33.613 -47.097 6.437 1 52.29 ? C6 ADP 998 X 1 HETATM 23 N N6 ADP . . . B 2 33.516 -48.345 6.956 1 52.3 ? N6 ADP 998 X 1 HETATM 24 N N1 ADP . . . B 2 32.518 -46.351 6.092 1 52.98 ? N1 ADP 998 X 1 HETATM 25 C C2 ADP . . . B 2 32.646 -45.094 5.584 1 53.36 ? C2 ADP 998 X 1 HETATM 26 N N3 ADP . . . B 2 33.856 -44.498 5.396 1 53.36 ? N3 ADP 998 X 1 HETATM 27 C C4 ADP . . . B 2 35.033 -45.144 5.691 1 52.6 ? C4 ADP 998 X 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #