data_2HVD # _model_server_result.job_id ADUcPoocGVy3y2i-Yyco8w _model_server_result.datetime_utc '2024-12-01 23:23:08' _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 2hvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":160}' # _entry.id 2HVD # _exptl.entry_id 2HVD _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 3 _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 2HVD _cell.length_a 114.26 _cell.length_b 114.26 _cell.length_c 89.789 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 114.26 114.26 44.8945 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 4 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 4 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 4 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 4 _struct_conn.ptnr2_symmetry 7_465 _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 2.056 _struct_conn.pdbx_value_order ? # _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 2HVD _atom_sites.fract_transf_matrix[1][1] 0.008752 _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] 0.008752 _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] 0.011137 _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 D 2 ADP A 1 160 160 ADP ADP . E 2 ADP B 1 160 160 ADP ADP . F 2 ADP C 1 160 160 ADP ADP . G 3 HOH A 1 161 3 HOH HOH . G 3 HOH A 2 162 4 HOH HOH . G 3 HOH A 3 163 14 HOH HOH . G 3 HOH A 4 164 15 HOH HOH . G 3 HOH A 5 165 21 HOH HOH . G 3 HOH A 6 166 22 HOH HOH . G 3 HOH A 7 167 27 HOH HOH . G 3 HOH A 8 168 28 HOH HOH . G 3 HOH A 9 169 30 HOH HOH . G 3 HOH A 10 170 34 HOH HOH . G 3 HOH A 11 171 35 HOH HOH . G 3 HOH A 12 172 47 HOH HOH . G 3 HOH A 13 173 49 HOH HOH . G 3 HOH A 14 174 51 HOH HOH . G 3 HOH A 15 175 53 HOH HOH . G 3 HOH A 16 176 54 HOH HOH . G 3 HOH A 17 177 55 HOH HOH . G 3 HOH A 18 178 67 HOH HOH . G 3 HOH A 19 179 68 HOH HOH . G 3 HOH A 20 180 94 HOH HOH . G 3 HOH A 21 181 95 HOH HOH . G 3 HOH A 22 182 107 HOH HOH . G 3 HOH A 23 183 115 HOH HOH . G 3 HOH A 24 184 118 HOH HOH . G 3 HOH A 25 185 119 HOH HOH . G 3 HOH A 26 186 120 HOH HOH . G 3 HOH A 27 187 130 HOH HOH . G 3 HOH A 28 188 138 HOH HOH . G 3 HOH A 29 189 146 HOH HOH . G 3 HOH A 30 190 153 HOH HOH . G 3 HOH A 31 191 165 HOH HOH . G 3 HOH A 32 192 168 HOH HOH . G 3 HOH A 33 193 169 HOH HOH . G 3 HOH A 34 194 170 HOH HOH . G 3 HOH A 35 195 180 HOH HOH . G 3 HOH A 36 196 184 HOH HOH . G 3 HOH A 37 197 185 HOH HOH . G 3 HOH A 38 198 186 HOH HOH . H 3 HOH B 1 161 1 HOH HOH . H 3 HOH B 2 162 5 HOH HOH . H 3 HOH B 3 163 7 HOH HOH . H 3 HOH B 4 164 8 HOH HOH . H 3 HOH B 5 165 9 HOH HOH . H 3 HOH B 6 166 10 HOH HOH . H 3 HOH B 7 167 23 HOH HOH . H 3 HOH B 8 168 24 HOH HOH . H 3 HOH B 9 169 25 HOH HOH . H 3 HOH B 10 170 26 HOH HOH . H 3 HOH B 11 171 32 HOH HOH . H 3 HOH B 12 172 33 HOH HOH . H 3 HOH B 13 173 36 HOH HOH . H 3 HOH B 14 174 37 HOH HOH . H 3 HOH B 15 175 38 HOH HOH . H 3 HOH B 16 176 39 HOH HOH . H 3 HOH B 17 177 40 HOH HOH . H 3 HOH B 18 178 41 HOH HOH . H 3 HOH B 19 179 42 HOH HOH . H 3 HOH B 20 180 43 HOH HOH . H 3 HOH B 21 181 44 HOH HOH . H 3 HOH B 22 182 48 HOH HOH . H 3 HOH B 23 183 52 HOH HOH . H 3 HOH B 24 184 57 HOH HOH . H 3 HOH B 25 185 58 HOH HOH . H 3 HOH B 26 186 59 HOH HOH . H 3 HOH B 27 187 60 HOH HOH . H 3 HOH B 28 188 61 HOH HOH . H 3 HOH B 29 189 62 HOH HOH . H 3 HOH B 30 190 76 HOH HOH . H 3 HOH B 31 191 80 HOH HOH . H 3 HOH B 32 192 84 HOH HOH . H 3 HOH B 33 193 87 HOH HOH . H 3 HOH B 34 194 88 HOH HOH . H 3 HOH B 35 195 89 HOH HOH . H 3 HOH B 36 196 90 HOH HOH . H 3 HOH B 37 197 91 HOH HOH . H 3 HOH B 38 198 93 HOH HOH . H 3 HOH B 39 199 96 HOH HOH . H 3 HOH B 40 200 97 HOH HOH . H 3 HOH B 41 201 99 HOH HOH . H 3 HOH B 42 202 100 HOH HOH . H 3 HOH B 43 203 101 HOH HOH . H 3 HOH B 44 204 102 HOH HOH . H 3 HOH B 45 205 103 HOH HOH . H 3 HOH B 46 206 104 HOH HOH . H 3 HOH B 47 207 105 HOH HOH . H 3 HOH B 48 208 109 HOH HOH . H 3 HOH B 49 209 110 HOH HOH . H 3 HOH B 50 210 114 HOH HOH . H 3 HOH B 51 211 116 HOH HOH . H 3 HOH B 52 212 117 HOH HOH . H 3 HOH B 53 213 123 HOH HOH . H 3 HOH B 54 214 125 HOH HOH . H 3 HOH B 55 215 127 HOH HOH . H 3 HOH B 56 216 128 HOH HOH . H 3 HOH B 57 217 131 HOH HOH . H 3 HOH B 58 218 132 HOH HOH . H 3 HOH B 59 219 135 HOH HOH . H 3 HOH B 60 220 136 HOH HOH . H 3 HOH B 61 221 137 HOH HOH . H 3 HOH B 62 222 139 HOH HOH . H 3 HOH B 63 223 142 HOH HOH . H 3 HOH B 64 224 143 HOH HOH . H 3 HOH B 65 225 144 HOH HOH . H 3 HOH B 66 226 145 HOH HOH . H 3 HOH B 67 227 147 HOH HOH . H 3 HOH B 68 228 148 HOH HOH . H 3 HOH B 69 229 150 HOH HOH . H 3 HOH B 70 230 151 HOH HOH . H 3 HOH B 71 231 152 HOH HOH . H 3 HOH B 72 232 156 HOH HOH . H 3 HOH B 73 233 158 HOH HOH . H 3 HOH B 74 234 159 HOH HOH . H 3 HOH B 75 235 160 HOH HOH . H 3 HOH B 76 236 161 HOH HOH . H 3 HOH B 77 237 162 HOH HOH . H 3 HOH B 78 238 173 HOH HOH . H 3 HOH B 79 239 174 HOH HOH . H 3 HOH B 80 240 175 HOH HOH . H 3 HOH B 81 241 176 HOH HOH . H 3 HOH B 82 242 177 HOH HOH . H 3 HOH B 83 243 178 HOH HOH . H 3 HOH B 84 244 179 HOH HOH . H 3 HOH B 85 245 181 HOH HOH . H 3 HOH B 86 246 182 HOH HOH . H 3 HOH B 87 247 183 HOH HOH . I 3 HOH C 1 161 2 HOH HOH . I 3 HOH C 2 162 6 HOH HOH . I 3 HOH C 3 163 11 HOH HOH . I 3 HOH C 4 164 12 HOH HOH . I 3 HOH C 5 165 13 HOH HOH . I 3 HOH C 6 166 16 HOH HOH . I 3 HOH C 7 167 17 HOH HOH . I 3 HOH C 8 168 18 HOH HOH . I 3 HOH C 9 169 19 HOH HOH . I 3 HOH C 10 170 20 HOH HOH . I 3 HOH C 11 171 29 HOH HOH . I 3 HOH C 12 172 31 HOH HOH . I 3 HOH C 13 173 45 HOH HOH . I 3 HOH C 14 174 46 HOH HOH . I 3 HOH C 15 175 50 HOH HOH . I 3 HOH C 16 176 56 HOH HOH . I 3 HOH C 17 177 63 HOH HOH . I 3 HOH C 18 178 64 HOH HOH . I 3 HOH C 19 179 65 HOH HOH . I 3 HOH C 20 180 66 HOH HOH . I 3 HOH C 21 181 69 HOH HOH . I 3 HOH C 22 182 70 HOH HOH . I 3 HOH C 23 183 71 HOH HOH . I 3 HOH C 24 184 72 HOH HOH . I 3 HOH C 25 185 73 HOH HOH . I 3 HOH C 26 186 74 HOH HOH . I 3 HOH C 27 187 75 HOH HOH . I 3 HOH C 28 188 77 HOH HOH . I 3 HOH C 29 189 78 HOH HOH . I 3 HOH C 30 190 79 HOH HOH . I 3 HOH C 31 191 81 HOH HOH . I 3 HOH C 32 192 82 HOH HOH . I 3 HOH C 33 193 83 HOH HOH . I 3 HOH C 34 194 85 HOH HOH . I 3 HOH C 35 195 86 HOH HOH . I 3 HOH C 36 196 92 HOH HOH . I 3 HOH C 37 197 98 HOH HOH . I 3 HOH C 38 198 106 HOH HOH . I 3 HOH C 39 199 108 HOH HOH . I 3 HOH C 40 200 111 HOH HOH . I 3 HOH C 41 201 112 HOH HOH . I 3 HOH C 42 202 113 HOH HOH . I 3 HOH C 43 203 121 HOH HOH . I 3 HOH C 44 204 122 HOH HOH . I 3 HOH C 45 205 124 HOH HOH . I 3 HOH C 46 206 126 HOH HOH . I 3 HOH C 47 207 129 HOH HOH . I 3 HOH C 48 208 133 HOH HOH . I 3 HOH C 49 209 134 HOH HOH . I 3 HOH C 50 210 140 HOH HOH . I 3 HOH C 51 211 141 HOH HOH . I 3 HOH C 52 212 149 HOH HOH . I 3 HOH C 53 213 154 HOH HOH . I 3 HOH C 54 214 155 HOH HOH . I 3 HOH C 55 215 157 HOH HOH . I 3 HOH C 56 216 163 HOH HOH . I 3 HOH C 57 217 164 HOH HOH . I 3 HOH C 58 218 166 HOH HOH . I 3 HOH C 59 219 167 HOH HOH . I 3 HOH C 60 220 171 HOH HOH . I 3 HOH C 61 221 172 HOH HOH . I 3 HOH C 62 222 187 HOH HOH . I 3 HOH C 63 223 188 HOH HOH . I 3 HOH C 64 224 189 HOH HOH . I 3 HOH C 65 225 190 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 . . . D 2 -10.043 95.921 15.436 1 63.23 ? PB ADP 160 A 1 HETATM 2 O O1B ADP . . . D 2 -10.564 96.701 14.25 1 65.82 ? O1B ADP 160 A 1 HETATM 3 O O2B ADP . . . D 2 -8.941 94.953 15.075 1 63.51 ? O2B ADP 160 A 1 HETATM 4 O O3B ADP . . . D 2 -9.791 96.787 16.654 1 62.21 ? O3B ADP 160 A 1 HETATM 5 P PA ADP . . . D 2 -12.809 95.17 15.857 1 61.78 ? PA ADP 160 A 1 HETATM 6 O O1A ADP . . . D 2 -13.116 96.52 15.246 1 62.5 ? O1A ADP 160 A 1 HETATM 7 O O2A ADP . . . D 2 -13.412 93.908 15.295 1 61.18 ? O2A ADP 160 A 1 HETATM 8 O O3A ADP . . . D 2 -11.218 94.894 15.854 1 63.49 ? O3A ADP 160 A 1 HETATM 9 O O5' ADP . . . D 2 -13.113 95.331 17.424 1 58.47 ? O5' ADP 160 A 1 HETATM 10 C C5' ADP . . . D 2 -12.761 96.572 18.02 1 58.43 ? C5' ADP 160 A 1 HETATM 11 C C4' ADP . . . D 2 -12.272 96.373 19.439 1 58.67 ? C4' ADP 160 A 1 HETATM 12 O O4' ADP . . . D 2 -13.237 95.608 20.164 1 58.43 ? O4' ADP 160 A 1 HETATM 13 C C3' ADP . . . D 2 -10.946 95.62 19.525 1 58.82 ? C3' ADP 160 A 1 HETATM 14 O O3' ADP . . . D 2 -9.812 96.503 19.467 1 57.75 ? O3' ADP 160 A 1 HETATM 15 C C2' ADP . . . D 2 -11.075 94.864 20.844 1 58.19 ? C2' ADP 160 A 1 HETATM 16 O O2' ADP . . . D 2 -10.53 95.59 21.96 1 57.89 ? O2' ADP 160 A 1 HETATM 17 C C1' ADP . . . D 2 -12.58 94.686 21.03 1 57.23 ? C1' ADP 160 A 1 HETATM 18 N N9 ADP . . . D 2 -13.001 93.317 20.666 1 55.3 ? N9 ADP 160 A 1 HETATM 19 C C8 ADP . . . D 2 -13.067 92.772 19.432 1 54.44 ? C8 ADP 160 A 1 HETATM 20 N N7 ADP . . . D 2 -13.499 91.485 19.495 1 53.79 ? N7 ADP 160 A 1 HETATM 21 C C5 ADP . . . D 2 -13.708 91.214 20.798 1 54.39 ? C5 ADP 160 A 1 HETATM 22 C C6 ADP . . . D 2 -14.161 90.057 21.584 1 54.26 ? C6 ADP 160 A 1 HETATM 23 N N6 ADP . . . D 2 -14.482 88.91 20.951 1 55.12 ? N6 ADP 160 A 1 HETATM 24 N N1 ADP . . . D 2 -14.245 90.188 22.925 1 53.77 ? N1 ADP 160 A 1 HETATM 25 C C2 ADP . . . D 2 -13.922 91.327 23.571 1 54.36 ? C2 ADP 160 A 1 HETATM 26 N N3 ADP . . . D 2 -13.502 92.426 22.927 1 54.62 ? N3 ADP 160 A 1 HETATM 27 C C4 ADP . . . D 2 -13.382 92.421 21.568 1 54.96 ? C4 ADP 160 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #