data_2NT8 # _model_server_result.job_id RA8b1_HYGleHLqENtVYydQ _model_server_result.datetime_utc '2024-11-25 02:53:15' _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 2nt8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":999}' # _entry.id 2NT8 # _exptl.entry_id 2NT8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 2NT8 _cell.length_a 110.609 _cell.length_b 110.609 _cell.length_c 110.609 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NT8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 OD1 ASN 191 A ASN 156 5_555 B MG MG . A MG 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc2 B MG MG . A MG 998 1_555 D O1B ATP . A ATP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc3 B MG MG . A MG 998 1_555 D O3G ATP . A ATP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc4 B MG MG . A MG 998 1_555 D O1A ATP . A ATP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc5 B MG MG . A MG 998 1_555 G O HOH . A HOH 1003 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc6 B MG MG . A MG 998 1_555 G O HOH . A HOH 1039 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 2NT8 _atom_sites.fract_transf_matrix[1][1] 0.009041 _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] 0.009041 _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] 0.009041 _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 MG A 1 998 998 MG MG . C 3 SO4 A 1 601 1 SO4 SO4 . D 4 ATP A 1 999 999 ATP ATP . E 5 GOL A 1 889 889 GOL GOL . F 5 GOL A 1 888 888 GOL GOL . G 6 HOH A 1 1000 1 HOH HOH . G 6 HOH A 2 1001 2 HOH HOH . G 6 HOH A 3 1002 3 HOH HOH . G 6 HOH A 4 1003 4 HOH HOH . G 6 HOH A 5 1004 5 HOH HOH . G 6 HOH A 6 1005 6 HOH HOH . G 6 HOH A 7 1006 7 HOH HOH . G 6 HOH A 8 1007 8 HOH HOH . G 6 HOH A 9 1008 9 HOH HOH . G 6 HOH A 10 1009 10 HOH HOH . G 6 HOH A 11 1010 11 HOH HOH . G 6 HOH A 12 1011 12 HOH HOH . G 6 HOH A 13 1012 13 HOH HOH . G 6 HOH A 14 1013 14 HOH HOH . G 6 HOH A 15 1014 15 HOH HOH . G 6 HOH A 16 1015 16 HOH HOH . G 6 HOH A 17 1016 17 HOH HOH . G 6 HOH A 18 1017 18 HOH HOH . G 6 HOH A 19 1018 19 HOH HOH . G 6 HOH A 20 1019 20 HOH HOH . G 6 HOH A 21 1020 21 HOH HOH . G 6 HOH A 22 1021 22 HOH HOH . G 6 HOH A 23 1022 23 HOH HOH . G 6 HOH A 24 1023 24 HOH HOH . G 6 HOH A 25 1024 25 HOH HOH . G 6 HOH A 26 1025 26 HOH HOH . G 6 HOH A 27 1026 27 HOH HOH . G 6 HOH A 28 1027 28 HOH HOH . G 6 HOH A 29 1028 29 HOH HOH . G 6 HOH A 30 1029 30 HOH HOH . G 6 HOH A 31 1030 31 HOH HOH . G 6 HOH A 32 1031 32 HOH HOH . G 6 HOH A 33 1032 33 HOH HOH . G 6 HOH A 34 1033 34 HOH HOH . G 6 HOH A 35 1034 35 HOH HOH . G 6 HOH A 36 1035 36 HOH HOH . G 6 HOH A 37 1036 37 HOH HOH . G 6 HOH A 38 1037 38 HOH HOH . G 6 HOH A 39 1038 39 HOH HOH . G 6 HOH A 40 1039 40 HOH HOH . G 6 HOH A 41 1040 41 HOH HOH . G 6 HOH A 42 1041 42 HOH HOH . G 6 HOH A 43 1042 43 HOH HOH . G 6 HOH A 44 1043 44 HOH HOH . G 6 HOH A 45 1044 45 HOH HOH . G 6 HOH A 46 1045 46 HOH HOH . G 6 HOH A 47 1046 47 HOH HOH . G 6 HOH A 48 1047 48 HOH HOH . G 6 HOH A 49 1048 49 HOH HOH . G 6 HOH A 50 1049 50 HOH HOH . G 6 HOH A 51 1050 51 HOH HOH . G 6 HOH A 52 1051 52 HOH HOH . G 6 HOH A 53 1052 53 HOH HOH . G 6 HOH A 54 1053 54 HOH HOH . G 6 HOH A 55 1054 55 HOH HOH . G 6 HOH A 56 1055 56 HOH HOH . G 6 HOH A 57 1056 57 HOH HOH . G 6 HOH A 58 1057 58 HOH HOH . G 6 HOH A 59 1058 59 HOH HOH . G 6 HOH A 60 1059 60 HOH HOH . G 6 HOH A 61 1060 61 HOH HOH . G 6 HOH A 62 1061 62 HOH HOH . G 6 HOH A 63 1062 63 HOH HOH . G 6 HOH A 64 1063 64 HOH HOH . G 6 HOH A 65 1064 65 HOH HOH . G 6 HOH A 66 1065 66 HOH HOH . G 6 HOH A 67 1066 67 HOH HOH . G 6 HOH A 68 1067 68 HOH HOH . G 6 HOH A 69 1068 69 HOH HOH . G 6 HOH A 70 1069 70 HOH HOH . G 6 HOH A 71 1070 71 HOH HOH . G 6 HOH A 72 1071 72 HOH HOH . G 6 HOH A 73 1072 73 HOH HOH . G 6 HOH A 74 1073 74 HOH HOH . G 6 HOH A 75 1074 75 HOH HOH . G 6 HOH A 76 1075 76 HOH HOH . G 6 HOH A 77 1076 77 HOH HOH . G 6 HOH A 78 1077 78 HOH HOH . G 6 HOH A 79 1078 79 HOH HOH . G 6 HOH A 80 1079 80 HOH HOH . G 6 HOH A 81 1080 81 HOH HOH . G 6 HOH A 82 1081 82 HOH HOH . G 6 HOH A 83 1082 83 HOH HOH . G 6 HOH A 84 1083 84 HOH HOH . G 6 HOH A 85 1084 85 HOH HOH . G 6 HOH A 86 1085 86 HOH HOH . G 6 HOH A 87 1086 87 HOH HOH . G 6 HOH A 88 1087 88 HOH HOH . G 6 HOH A 89 1088 89 HOH HOH . G 6 HOH A 90 1089 90 HOH HOH . G 6 HOH A 91 1090 91 HOH HOH . G 6 HOH A 92 1091 92 HOH HOH . G 6 HOH A 93 1092 93 HOH HOH . G 6 HOH A 94 1093 94 HOH HOH . G 6 HOH A 95 1094 95 HOH HOH . G 6 HOH A 96 1095 96 HOH HOH . G 6 HOH A 97 1096 97 HOH HOH . G 6 HOH A 98 1097 98 HOH HOH . G 6 HOH A 99 1098 99 HOH HOH . G 6 HOH A 100 1099 100 HOH HOH . G 6 HOH A 101 1100 101 HOH HOH . G 6 HOH A 102 1101 102 HOH HOH . G 6 HOH A 103 1102 103 HOH HOH . G 6 HOH A 104 1103 104 HOH HOH . G 6 HOH A 105 1104 105 HOH HOH . G 6 HOH A 106 1105 106 HOH HOH . G 6 HOH A 107 1106 107 HOH HOH . G 6 HOH A 108 1107 108 HOH HOH . G 6 HOH A 109 1108 109 HOH HOH . G 6 HOH A 110 1109 110 HOH HOH . G 6 HOH A 111 1110 111 HOH HOH . G 6 HOH A 112 1111 112 HOH HOH . G 6 HOH A 113 1112 113 HOH HOH . G 6 HOH A 114 1113 114 HOH HOH . G 6 HOH A 115 1114 115 HOH HOH . G 6 HOH A 116 1115 116 HOH HOH . G 6 HOH A 117 1116 117 HOH HOH . G 6 HOH A 118 1117 118 HOH HOH . G 6 HOH A 119 1118 119 HOH HOH . G 6 HOH A 120 1119 120 HOH HOH . G 6 HOH A 121 1120 121 HOH HOH . G 6 HOH A 122 1121 122 HOH HOH . G 6 HOH A 123 1122 123 HOH HOH . G 6 HOH A 124 1123 124 HOH HOH . G 6 HOH A 125 1124 125 HOH HOH . G 6 HOH A 126 1125 126 HOH HOH . G 6 HOH A 127 1126 127 HOH HOH . G 6 HOH A 128 1127 128 HOH HOH . G 6 HOH A 129 1128 129 HOH HOH . G 6 HOH A 130 1129 130 HOH HOH . G 6 HOH A 131 1130 131 HOH HOH . G 6 HOH A 132 1131 132 HOH HOH . G 6 HOH A 133 1132 133 HOH HOH . G 6 HOH A 134 1133 134 HOH HOH . G 6 HOH A 135 1134 135 HOH HOH . G 6 HOH A 136 1135 136 HOH HOH . G 6 HOH A 137 1136 137 HOH HOH . G 6 HOH A 138 1137 138 HOH HOH . G 6 HOH A 139 1138 139 HOH HOH . G 6 HOH A 140 1139 140 HOH HOH . G 6 HOH A 141 1140 141 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 PG ATP . . . D 4 32.938 9.459 4.71 1 19.12 ? PG ATP 999 A 1 HETATM 2 O O1G ATP . . . D 4 34.386 9.046 4.899 1 21.49 ? O1G ATP 999 A 1 HETATM 3 O O2G ATP . . . D 4 32.568 9.689 3.284 1 17.36 ? O2G ATP 999 A 1 HETATM 4 O O3G ATP . . . D 4 32.505 10.569 5.635 1 14.58 ? O3G ATP 999 A 1 HETATM 5 P PB ATP . . . D 4 30.751 7.929 5.843 1 16.38 ? PB ATP 999 A 1 HETATM 6 O O1B ATP . . . D 4 30.017 9.229 5.705 1 14.02 ? O1B ATP 999 A 1 HETATM 7 O O2B ATP . . . D 4 30.106 6.674 5.292 1 16.91 ? O2B ATP 999 A 1 HETATM 8 O O3B ATP . . . D 4 32.198 8.095 5.149 1 18.32 ? O3B ATP 999 A 1 HETATM 9 P PA ATP . . . D 4 31.722 8.499 8.507 1 18 ? PA ATP 999 A 1 HETATM 10 O O1A ATP . . . D 4 31.304 9.913 8.266 1 15.4 ? O1A ATP 999 A 1 HETATM 11 O O2A ATP . . . D 4 33.196 8.201 8.629 1 20.55 ? O2A ATP 999 A 1 HETATM 12 O O3A ATP . . . D 4 31.148 7.515 7.347 1 16.82 ? O3A ATP 999 A 1 HETATM 13 O O5' ATP . . . D 4 30.969 7.98 9.823 1 17.8 ? O5' ATP 999 A 1 HETATM 14 C C5' ATP . . . D 4 31.378 6.892 10.649 1 15.93 ? C5' ATP 999 A 1 HETATM 15 C C4' ATP . . . D 4 30.204 5.977 10.931 1 17.55 ? C4' ATP 999 A 1 HETATM 16 O O4' ATP . . . D 4 29.087 6.682 11.499 1 16.61 ? O4' ATP 999 A 1 HETATM 17 C C3' ATP . . . D 4 29.701 5.319 9.661 1 16.27 ? C3' ATP 999 A 1 HETATM 18 O O3' ATP . . . D 4 30.438 4.128 9.356 1 19.23 ? O3' ATP 999 A 1 HETATM 19 C C2' ATP . . . D 4 28.241 5.044 9.968 1 14.77 ? C2' ATP 999 A 1 HETATM 20 O O2' ATP . . . D 4 28.046 3.864 10.772 1 16.59 ? O2' ATP 999 A 1 HETATM 21 C C1' ATP . . . D 4 27.872 6.221 10.866 1 14.55 ? C1' ATP 999 A 1 HETATM 22 N N9 ATP . . . D 4 27.386 7.398 10.136 1 14.39 ? N9 ATP 999 A 1 HETATM 23 C C8 ATP . . . D 4 27.877 7.95 9.017 1 15.08 ? C8 ATP 999 A 1 HETATM 24 N N7 ATP . . . D 4 27.194 9.042 8.682 1 14.98 ? N7 ATP 999 A 1 HETATM 25 C C5 ATP . . . D 4 26.25 9.226 9.635 1 14.21 ? C5 ATP 999 A 1 HETATM 26 C C6 ATP . . . D 4 25.194 10.21 9.869 1 10.79 ? C6 ATP 999 A 1 HETATM 27 N N6 ATP . . . D 4 24.994 11.262 9.042 1 12.26 ? N6 ATP 999 A 1 HETATM 28 N N1 ATP . . . D 4 24.42 10.015 10.976 1 13.02 ? N1 ATP 999 A 1 HETATM 29 C C2 ATP . . . D 4 24.602 8.991 11.849 1 14.2 ? C2 ATP 999 A 1 HETATM 30 N N3 ATP . . . D 4 25.558 8.045 11.679 1 13.27 ? N3 ATP 999 A 1 HETATM 31 C C4 ATP . . . D 4 26.379 8.138 10.593 1 13.84 ? C4 ATP 999 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #