data_3NHA # _model_server_result.job_id DT8a0C4y79v8or67NxqKxA _model_server_result.datetime_utc '2024-12-26 12:30:18' _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 3nha # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2}' # _entry.id 3NHA # _exptl.entry_id 3NHA _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 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 3NHA _cell.length_a 56.272 _cell.length_b 70.708 _cell.length_c 71.113 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NHA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,G _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 3 _struct_asym.id C _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 C O2B ADP . A ADP 2 1_555 D MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc2 D MG MG . A MG 3 1_555 G O HOH . A HOH 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc3 D MG MG . A MG 3 1_555 G O HOH . A HOH 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc4 D MG MG . A MG 3 1_555 G O HOH . A HOH 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc5 D MG MG . A MG 3 1_555 G O HOH . A HOH 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? # _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 3NHA _atom_sites.fract_transf_matrix[1][1] 0.017771 _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] 0.014143 _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] 0.014062 _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 PO4 A 1 1 1 PO4 PO4 . C 3 ADP A 1 2 2 ADP ADP . D 4 MG A 1 3 3 MG MG . E 5 BME A 1 4 4 BME BME . F 5 BME A 1 5 5 BME BME . G 6 HOH A 1 6 6 HOH HOH . G 6 HOH A 2 7 7 HOH HOH . G 6 HOH A 3 8 8 HOH HOH . G 6 HOH A 4 9 9 HOH HOH . G 6 HOH A 5 10 10 HOH HOH . G 6 HOH A 6 11 11 HOH HOH . G 6 HOH A 7 12 12 HOH HOH . G 6 HOH A 8 13 13 HOH HOH . G 6 HOH A 9 14 14 HOH HOH . G 6 HOH A 10 15 15 HOH HOH . G 6 HOH A 11 16 16 HOH HOH . G 6 HOH A 12 17 17 HOH HOH . G 6 HOH A 13 18 18 HOH HOH . G 6 HOH A 14 19 19 HOH HOH . G 6 HOH A 15 20 20 HOH HOH . G 6 HOH A 16 21 21 HOH HOH . G 6 HOH A 17 22 22 HOH HOH . G 6 HOH A 18 23 23 HOH HOH . G 6 HOH A 19 24 24 HOH HOH . G 6 HOH A 20 25 25 HOH HOH . G 6 HOH A 21 26 26 HOH HOH . G 6 HOH A 22 27 27 HOH HOH . G 6 HOH A 23 28 28 HOH HOH . G 6 HOH A 24 29 29 HOH HOH . G 6 HOH A 25 30 30 HOH HOH . G 6 HOH A 26 31 31 HOH HOH . G 6 HOH A 27 32 32 HOH HOH . G 6 HOH A 28 33 33 HOH HOH . G 6 HOH A 29 34 34 HOH HOH . G 6 HOH A 30 35 35 HOH HOH . G 6 HOH A 31 36 36 HOH HOH . G 6 HOH A 32 37 37 HOH HOH . G 6 HOH A 33 38 38 HOH HOH . G 6 HOH A 34 39 39 HOH HOH . G 6 HOH A 35 40 40 HOH HOH . G 6 HOH A 36 41 41 HOH HOH . G 6 HOH A 37 42 42 HOH HOH . G 6 HOH A 38 43 43 HOH HOH . G 6 HOH A 39 44 44 HOH HOH . G 6 HOH A 40 45 45 HOH HOH . G 6 HOH A 41 46 46 HOH HOH . G 6 HOH A 42 47 47 HOH HOH . G 6 HOH A 43 48 48 HOH HOH . G 6 HOH A 44 49 49 HOH HOH . G 6 HOH A 45 50 50 HOH HOH . G 6 HOH A 46 51 51 HOH HOH . G 6 HOH A 47 52 52 HOH HOH . G 6 HOH A 48 53 53 HOH HOH . G 6 HOH A 49 54 54 HOH HOH . G 6 HOH A 50 55 55 HOH HOH . G 6 HOH A 51 56 56 HOH HOH . G 6 HOH A 52 57 57 HOH HOH . G 6 HOH A 53 58 58 HOH HOH . G 6 HOH A 54 59 59 HOH HOH . G 6 HOH A 55 60 60 HOH HOH . G 6 HOH A 56 61 61 HOH HOH . G 6 HOH A 57 62 62 HOH HOH . G 6 HOH A 58 63 63 HOH HOH . G 6 HOH A 59 64 64 HOH HOH . G 6 HOH A 60 65 65 HOH HOH . G 6 HOH A 61 66 66 HOH HOH . G 6 HOH A 62 67 67 HOH HOH . G 6 HOH A 63 68 68 HOH HOH . G 6 HOH A 64 69 69 HOH HOH . G 6 HOH A 65 70 70 HOH HOH . G 6 HOH A 66 71 71 HOH HOH . G 6 HOH A 67 72 72 HOH HOH . G 6 HOH A 68 73 73 HOH HOH . G 6 HOH A 69 74 74 HOH HOH . G 6 HOH A 70 75 75 HOH HOH . G 6 HOH A 71 76 76 HOH HOH . G 6 HOH A 72 77 77 HOH HOH . G 6 HOH A 73 78 78 HOH HOH . G 6 HOH A 74 79 79 HOH HOH . G 6 HOH A 75 80 80 HOH HOH . G 6 HOH A 76 81 81 HOH HOH . G 6 HOH A 77 82 82 HOH HOH . G 6 HOH A 78 83 83 HOH HOH . G 6 HOH A 79 84 84 HOH HOH . G 6 HOH A 80 85 85 HOH HOH . G 6 HOH A 81 86 86 HOH HOH . G 6 HOH A 82 87 87 HOH HOH . G 6 HOH A 83 88 88 HOH HOH . G 6 HOH A 84 89 89 HOH HOH . G 6 HOH A 85 90 90 HOH HOH . G 6 HOH A 86 91 91 HOH HOH . G 6 HOH A 87 92 92 HOH HOH . G 6 HOH A 88 93 93 HOH HOH . G 6 HOH A 89 94 94 HOH HOH . G 6 HOH A 90 95 95 HOH HOH . G 6 HOH A 91 96 96 HOH HOH . G 6 HOH A 92 97 97 HOH HOH . G 6 HOH A 93 98 98 HOH HOH . G 6 HOH A 94 99 99 HOH HOH . G 6 HOH A 95 100 100 HOH HOH . G 6 HOH A 96 101 101 HOH HOH . G 6 HOH A 97 102 102 HOH HOH . G 6 HOH A 98 103 103 HOH HOH . G 6 HOH A 99 104 104 HOH HOH . G 6 HOH A 100 105 105 HOH HOH . G 6 HOH A 101 106 106 HOH HOH . G 6 HOH A 102 107 107 HOH HOH . G 6 HOH A 103 108 108 HOH HOH . G 6 HOH A 104 109 109 HOH HOH . G 6 HOH A 105 110 110 HOH HOH . G 6 HOH A 106 111 111 HOH HOH . G 6 HOH A 107 112 112 HOH HOH . G 6 HOH A 108 113 113 HOH HOH . G 6 HOH A 109 114 114 HOH HOH . G 6 HOH A 110 115 115 HOH HOH . G 6 HOH A 111 116 116 HOH HOH . G 6 HOH A 112 117 117 HOH HOH . G 6 HOH A 113 118 118 HOH HOH . G 6 HOH A 114 119 119 HOH HOH . G 6 HOH A 115 120 120 HOH HOH . G 6 HOH A 116 121 121 HOH HOH . G 6 HOH A 117 122 122 HOH HOH . G 6 HOH A 118 123 123 HOH HOH . G 6 HOH A 119 124 124 HOH HOH . G 6 HOH A 120 125 125 HOH HOH . G 6 HOH A 121 126 126 HOH HOH . G 6 HOH A 122 127 127 HOH HOH . G 6 HOH A 123 128 128 HOH HOH . G 6 HOH A 124 129 129 HOH HOH . G 6 HOH A 125 130 130 HOH HOH . G 6 HOH A 126 131 131 HOH HOH . G 6 HOH A 127 132 132 HOH HOH . G 6 HOH A 128 133 133 HOH HOH . G 6 HOH A 129 134 134 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 . . . C 3 24.105 -13.719 -10.29 1 23.81 ? PB ADP 2 A 1 HETATM 2 O O1B ADP . . . C 3 23.919 -12.419 -9.524 1 22.15 ? O1B ADP 2 A 1 HETATM 3 O O2B ADP . . . C 3 25.447 -14.374 -10.173 1 24.58 ? O2B ADP 2 A 1 HETATM 4 O O3B ADP . . . C 3 23.012 -14.757 -10.15 1 23.79 ? O3B ADP 2 A 1 HETATM 5 P PA ADP . . . C 3 24.197 -11.959 -12.632 1 27.52 ? PA ADP 2 A 1 HETATM 6 O O1A ADP . . . C 3 25.426 -11.352 -12.019 1 32.41 ? O1A ADP 2 A 1 HETATM 7 O O2A ADP . . . C 3 22.895 -11.179 -12.596 1 30.23 ? O2A ADP 2 A 1 HETATM 8 O O3A ADP . . . C 3 23.927 -13.326 -11.851 1 26.52 ? O3A ADP 2 A 1 HETATM 9 O O5' ADP . . . C 3 24.554 -12.443 -14.095 1 27.75 ? O5' ADP 2 A 1 HETATM 10 C C5' ADP . . . C 3 23.492 -12.873 -14.947 1 31.13 ? C5' ADP 2 A 1 HETATM 11 C C4' ADP . . . C 3 24.037 -13.21 -16.328 1 33.36 ? C4' ADP 2 A 1 HETATM 12 O O4' ADP . . . C 3 24.258 -11.984 -17.025 1 32.32 ? O4' ADP 2 A 1 HETATM 13 C C3' ADP . . . C 3 25.367 -13.956 -16.245 1 34.3 ? C3' ADP 2 A 1 HETATM 14 O O3' ADP . . . C 3 25.366 -14.892 -17.301 1 39.03 ? O3' ADP 2 A 1 HETATM 15 C C2' ADP . . . C 3 26.41 -12.922 -16.549 1 36.51 ? C2' ADP 2 A 1 HETATM 16 O O2' ADP . . . C 3 27.496 -13.513 -17.243 1 38.88 ? O2' ADP 2 A 1 HETATM 17 C C1' ADP . . . C 3 25.649 -11.924 -17.414 1 35.71 ? C1' ADP 2 A 1 HETATM 18 N N9 ADP . . . C 3 26.08 -10.544 -17.175 1 37.06 ? N9 ADP 2 A 1 HETATM 19 C C8 ADP . . . C 3 26.172 -9.93 -15.976 1 36.1 ? C8 ADP 2 A 1 HETATM 20 N N7 ADP . . . C 3 26.574 -8.653 -16.14 1 36.83 ? N7 ADP 2 A 1 HETATM 21 C C5 ADP . . . C 3 26.733 -8.473 -17.467 1 35.79 ? C5 ADP 2 A 1 HETATM 22 C C6 ADP . . . C 3 27.173 -7.365 -18.295 1 38.97 ? C6 ADP 2 A 1 HETATM 23 N N6 ADP . . . C 3 27.472 -6.215 -17.637 1 42.32 ? N6 ADP 2 A 1 HETATM 24 N N1 ADP . . . C 3 27.222 -7.537 -19.648 1 38.07 ? N1 ADP 2 A 1 HETATM 25 C C2 ADP . . . C 3 26.904 -8.716 -20.232 1 37.48 ? C2 ADP 2 A 1 HETATM 26 N N3 ADP . . . C 3 26.505 -9.801 -19.532 1 37.21 ? N3 ADP 2 A 1 HETATM 27 C C4 ADP . . . C 3 26.416 -9.711 -18.162 1 37.38 ? C4 ADP 2 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #