data_2XZO # _model_server_result.job_id XhR-Rx547883REfpzSt7Bg _model_server_result.datetime_utc '2024-11-24 16:18:19' _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 2xzo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1004}' # _entry.id 2XZO # _exptl.entry_id 2XZO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 2XZO _cell.length_a 77.066 _cell.length_b 101.896 _cell.length_c 112.32 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XZO _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 4 _struct_asym.id F _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 208 A THR 499 1_555 H MG MG . A MG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc2 A O MET 516 A MET 807 1_555 I MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? metalc ? metalc3 F O2B ADP . A ADP 1004 1_555 H MG MG . A MG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc4 H MG MG . A MG 1006 1_555 J O HOH . A HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc5 H MG MG . A MG 1006 1_555 J O HOH . A HOH 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc6 H MG MG . A MG 1006 1_555 J O HOH . A HOH 1195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? # _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 38 n n PB O2B ADP sing 39 n n PB O3B ADP sing 40 n n PB O3A ADP sing 41 n n O2B HOB2 ADP sing 42 n n O3B HOB3 ADP sing 43 n n PA O1A ADP doub 44 n n PA O2A ADP sing 45 n n PA O3A ADP sing 46 n n PA O5' ADP sing 47 n n O2A HOA2 ADP sing 48 n n O5' C5' ADP sing 49 n n C5' C4' ADP sing 50 n n C5' "H5'1" ADP sing 51 n n C5' "H5'2" ADP sing 52 n n C4' O4' ADP sing 53 n n C4' C3' ADP sing 54 n n C4' H4' ADP sing 55 n n O4' C1' ADP sing 56 n n C3' O3' ADP sing 57 n n C3' C2' ADP sing 58 n n C3' H3' ADP sing 59 n n O3' HO3' ADP sing 60 n n C2' O2' ADP sing 61 n n C2' C1' ADP sing 62 n n C2' H2' ADP sing 63 n n O2' HO2' ADP sing 64 n n C1' N9 ADP sing 65 n n C1' H1' ADP sing 66 n n N9 C8 ADP sing 67 n y N9 C4 ADP sing 68 n y C8 N7 ADP doub 69 n y C8 H8 ADP sing 70 n n N7 C5 ADP sing 71 n y C5 C6 ADP sing 72 n y C5 C4 ADP doub 73 n y C6 N6 ADP sing 74 n n C6 N1 ADP doub 75 n y N6 HN61 ADP sing 76 n n N6 HN62 ADP sing 77 n n N1 C2 ADP sing 78 n y C2 N3 ADP doub 79 n y C2 H2 ADP sing 80 n n N3 C4 ADP sing 81 n y # _atom_sites.entry_id 2XZO _atom_sites.fract_transf_matrix[1][1] 0.012976 _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] 0.009814 _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] 0.008903 _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 C 3 1PE A 1 1001 1 1PE 1PE . D 3 1PE A 1 1002 2 1PE 1PE . E 3 1PE A 1 1003 6 1PE 1PE . F 4 ADP A 1 1004 480 ADP ADP . G 5 ALF A 1 1005 481 ALF ALF . H 6 MG A 1 1006 482 MG MG . I 6 MG A 1 1007 483 MG MG . J 7 HOH A 1 1101 2110 HOH HOH . J 7 HOH A 2 1102 2002 HOH HOH . J 7 HOH A 3 1103 2080 HOH HOH . J 7 HOH A 4 1104 2085 HOH HOH . J 7 HOH A 5 1105 2072 HOH HOH . J 7 HOH A 6 1106 2077 HOH HOH . J 7 HOH A 7 1107 2084 HOH HOH . J 7 HOH A 8 1108 2061 HOH HOH . J 7 HOH A 9 1109 2043 HOH HOH . J 7 HOH A 10 1110 2094 HOH HOH . J 7 HOH A 11 1111 2115 HOH HOH . J 7 HOH A 12 1112 2062 HOH HOH . J 7 HOH A 13 1113 2109 HOH HOH . J 7 HOH A 14 1114 2106 HOH HOH . J 7 HOH A 15 1115 2118 HOH HOH . J 7 HOH A 16 1116 2090 HOH HOH . J 7 HOH A 17 1117 2083 HOH HOH . J 7 HOH A 18 1118 2113 HOH HOH . J 7 HOH A 19 1119 2001 HOH HOH . J 7 HOH A 20 1120 2018 HOH HOH . J 7 HOH A 21 1121 2046 HOH HOH . J 7 HOH A 22 1122 2020 HOH HOH . J 7 HOH A 23 1123 2070 HOH HOH . J 7 HOH A 24 1124 2081 HOH HOH . J 7 HOH A 25 1125 2047 HOH HOH . J 7 HOH A 26 1126 2092 HOH HOH . J 7 HOH A 27 1127 2088 HOH HOH . J 7 HOH A 28 1128 2064 HOH HOH . J 7 HOH A 29 1129 2007 HOH HOH . J 7 HOH A 30 1130 2116 HOH HOH . J 7 HOH A 31 1131 2013 HOH HOH . J 7 HOH A 32 1132 2051 HOH HOH . J 7 HOH A 33 1133 2093 HOH HOH . J 7 HOH A 34 1134 2002 HOH HOH . J 7 HOH A 35 1135 2010 HOH HOH . J 7 HOH A 36 1136 2034 HOH HOH . J 7 HOH A 37 1137 2041 HOH HOH . J 7 HOH A 38 1138 2025 HOH HOH . J 7 HOH A 39 1139 2058 HOH HOH . J 7 HOH A 40 1140 2028 HOH HOH . J 7 HOH A 41 1141 2082 HOH HOH . J 7 HOH A 42 1142 2073 HOH HOH . J 7 HOH A 43 1143 2089 HOH HOH . J 7 HOH A 44 1144 2015 HOH HOH . J 7 HOH A 45 1145 2060 HOH HOH . J 7 HOH A 46 1146 2091 HOH HOH . J 7 HOH A 47 1147 2022 HOH HOH . J 7 HOH A 48 1148 2049 HOH HOH . J 7 HOH A 49 1149 2066 HOH HOH . J 7 HOH A 50 1150 2100 HOH HOH . J 7 HOH A 51 1151 2075 HOH HOH . J 7 HOH A 52 1152 2059 HOH HOH . J 7 HOH A 53 1153 2095 HOH HOH . J 7 HOH A 54 1154 2006 HOH HOH . J 7 HOH A 55 1155 2112 HOH HOH . J 7 HOH A 56 1156 2040 HOH HOH . J 7 HOH A 57 1157 2009 HOH HOH . J 7 HOH A 58 1158 2031 HOH HOH . J 7 HOH A 59 1159 2098 HOH HOH . J 7 HOH A 60 1160 2004 HOH HOH . J 7 HOH A 61 1161 2035 HOH HOH . J 7 HOH A 62 1162 2096 HOH HOH . J 7 HOH A 63 1163 2048 HOH HOH . J 7 HOH A 64 1164 2074 HOH HOH . J 7 HOH A 65 1165 2002 HOH HOH . J 7 HOH A 66 1166 2078 HOH HOH . J 7 HOH A 67 1167 2117 HOH HOH . J 7 HOH A 68 1168 2027 HOH HOH . J 7 HOH A 69 1169 2079 HOH HOH . J 7 HOH A 70 1170 2102 HOH HOH . J 7 HOH A 71 1171 2014 HOH HOH . J 7 HOH A 72 1172 2056 HOH HOH . J 7 HOH A 73 1173 2068 HOH HOH . J 7 HOH A 74 1174 2057 HOH HOH . J 7 HOH A 75 1175 2001 HOH HOH . J 7 HOH A 76 1176 2008 HOH HOH . J 7 HOH A 77 1177 2032 HOH HOH . J 7 HOH A 78 1178 2055 HOH HOH . J 7 HOH A 79 1179 2050 HOH HOH . J 7 HOH A 80 1180 2086 HOH HOH . J 7 HOH A 81 1181 2037 HOH HOH . J 7 HOH A 82 1182 2016 HOH HOH . J 7 HOH A 83 1183 2044 HOH HOH . J 7 HOH A 84 1184 2114 HOH HOH . J 7 HOH A 85 1185 2063 HOH HOH . J 7 HOH A 86 1186 2101 HOH HOH . J 7 HOH A 87 1187 2052 HOH HOH . J 7 HOH A 88 1188 2108 HOH HOH . J 7 HOH A 89 1189 2001 HOH HOH . J 7 HOH A 90 1190 2030 HOH HOH . J 7 HOH A 91 1191 2038 HOH HOH . J 7 HOH A 92 1192 2026 HOH HOH . J 7 HOH A 93 1193 2024 HOH HOH . J 7 HOH A 94 1194 2104 HOH HOH . J 7 HOH A 95 1195 2054 HOH HOH . J 7 HOH A 96 1196 2021 HOH HOH . J 7 HOH A 97 1197 2042 HOH HOH . J 7 HOH A 98 1198 2033 HOH HOH . J 7 HOH A 99 1199 2097 HOH HOH . J 7 HOH A 100 1200 2003 HOH HOH . J 7 HOH A 101 1201 2111 HOH HOH . J 7 HOH A 102 1202 2067 HOH HOH . J 7 HOH A 103 1203 2036 HOH HOH . J 7 HOH A 104 1204 2005 HOH HOH . J 7 HOH A 105 1205 2039 HOH HOH . J 7 HOH A 106 1206 2071 HOH HOH . J 7 HOH A 107 1207 2107 HOH HOH . J 7 HOH A 108 1208 2069 HOH HOH . J 7 HOH A 109 1209 2076 HOH HOH . J 7 HOH A 110 1210 2045 HOH HOH . J 7 HOH A 111 1211 2099 HOH HOH . J 7 HOH A 112 1212 2029 HOH HOH . J 7 HOH A 113 1213 2017 HOH HOH . J 7 HOH A 114 1214 2019 HOH HOH . J 7 HOH A 115 1215 2012 HOH HOH . J 7 HOH A 116 1216 2105 HOH HOH . J 7 HOH A 117 1217 2065 HOH HOH . J 7 HOH A 118 1218 2103 HOH HOH . J 7 HOH A 119 1219 2087 HOH HOH . J 7 HOH A 120 1220 2011 HOH HOH . J 7 HOH A 121 1221 2053 HOH HOH . J 7 HOH A 122 1222 2023 HOH HOH . K 7 HOH D 1 101 2002 HOH HOH . K 7 HOH D 2 102 2003 HOH HOH . K 7 HOH D 3 103 2001 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 . . . F 4 -7.387 -19.895 -14.57 1 21.3 ? PB ADP 1004 A 1 HETATM 2 O O1B ADP . . . F 4 -7.277 -19.603 -16.076 1 26.91 ? O1B ADP 1004 A 1 HETATM 3 O O2B ADP . . . F 4 -6.195 -19.312 -13.782 1 21.57 ? O2B ADP 1004 A 1 HETATM 4 O O3B ADP . . . F 4 -7.476 -21.406 -14.367 1 23.14 ? O3B ADP 1004 A 1 HETATM 5 P PA ADP . . . F 4 -8.686 -17.939 -13.066 1 18.62 ? PA ADP 1004 A 1 HETATM 6 O O1A ADP . . . F 4 -8.284 -16.684 -13.866 1 24.44 ? O1A ADP 1004 A 1 HETATM 7 O O2A ADP . . . F 4 -7.798 -18.053 -11.858 1 20.01 ? O2A ADP 1004 A 1 HETATM 8 O O3A ADP . . . F 4 -8.676 -19.212 -14.025 1 26.98 ? O3A ADP 1004 A 1 HETATM 9 O O5' ADP . . . F 4 -10.185 -17.855 -12.589 1 28.7 ? O5' ADP 1004 A 1 HETATM 10 C C5' ADP . . . F 4 -11.162 -17.673 -13.551 1 22.51 ? C5' ADP 1004 A 1 HETATM 11 C C4' ADP . . . F 4 -12.368 -16.923 -13.035 1 27.49 ? C4' ADP 1004 A 1 HETATM 12 O O4' ADP . . . F 4 -13.319 -17.694 -12.238 1 23.82 ? O4' ADP 1004 A 1 HETATM 13 C C3' ADP . . . F 4 -12.216 -15.617 -12.305 1 25.58 ? C3' ADP 1004 A 1 HETATM 14 O O3' ADP . . . F 4 -13.01 -14.553 -12.667 1 26.53 ? O3' ADP 1004 A 1 HETATM 15 C C2' ADP . . . F 4 -12.216 -16.01 -10.879 1 19.81 ? C2' ADP 1004 A 1 HETATM 16 O O2' ADP . . . F 4 -12.339 -15.04 -9.88 1 26.94 ? O2' ADP 1004 A 1 HETATM 17 C C1' ADP . . . F 4 -13.169 -17.198 -10.839 1 21.43 ? C1' ADP 1004 A 1 HETATM 18 N N9 ADP . . . F 4 -13.084 -18.214 -9.841 1 25.11 ? N9 ADP 1004 A 1 HETATM 19 C C8 ADP . . . F 4 -11.998 -19.186 -9.689 1 23.01 ? C8 ADP 1004 A 1 HETATM 20 N N7 ADP . . . F 4 -12.285 -19.939 -8.653 1 23.65 ? N7 ADP 1004 A 1 HETATM 21 C C5 ADP . . . F 4 -13.565 -19.471 -8.113 1 23.99 ? C5 ADP 1004 A 1 HETATM 22 C C6 ADP . . . F 4 -14.346 -19.912 -6.987 1 24.11 ? C6 ADP 1004 A 1 HETATM 23 N N6 ADP . . . F 4 -13.857 -20.966 -6.174 1 23.48 ? N6 ADP 1004 A 1 HETATM 24 N N1 ADP . . . F 4 -15.581 -19.28 -6.666 1 34.89 ? N1 ADP 1004 A 1 HETATM 25 C C2 ADP . . . F 4 -16.038 -18.203 -7.465 1 26.05 ? C2 ADP 1004 A 1 HETATM 26 N N3 ADP . . . F 4 -15.291 -17.758 -8.55 1 24.55 ? N3 ADP 1004 A 1 HETATM 27 C C4 ADP . . . F 4 -14.007 -18.432 -8.863 1 24.85 ? C4 ADP 1004 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 216 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #