data_3NBA # _model_server_result.job_id LV5vIFvnIs3jVT_LRDD47g _model_server_result.datetime_utc '2024-11-28 03:31:38' _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 3nba # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":200}' # _entry.id 3NBA # _exptl.entry_id 3NBA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _entity.pdbx_number_of_molecules 4 _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 3NBA _cell.length_a 115.118 _cell.length_b 115.118 _cell.length_c 133.913 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NBA _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,H,I,L,N 1 1,2,3 B,D,G,J,K,M,O 2 1,4,5 # 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' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 57.559 -99.695112 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 115.118 0 0 4 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -57.559 -99.695112 0 5 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 57.559 -99.695112 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 H N N ? 2 J N 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 F MG MG . A MG 158 1_555 L O HOH . A HOH 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc2 F MG MG . A MG 158 1_555 E O1G APC . A APC 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc3 F MG MG . A MG 158 1_555 E O2A APC . A APC 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc4 I MG MG . C MG 158 1_555 H O1G APC . C APC 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc5 I MG MG . C MG 158 1_555 H O2A APC . C APC 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc6 K MG MG . D MG 158 1_555 J O2A APC . D APC 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc7 K MG MG . D MG 158 1_555 J O1G APC . D APC 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 3NBA _atom_sites.fract_transf_matrix[1][1] 0.008687 _atom_sites.fract_transf_matrix[1][2] 0.005015 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010031 _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] 0.007468 _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 E 2 APC A 1 200 200 APC APC . F 3 MG A 1 158 1 MG MG . G 2 APC B 1 200 200 APC APC . H 2 APC C 1 200 200 APC APC . I 3 MG C 1 158 1 MG MG . J 2 APC D 1 200 200 APC APC . K 3 MG D 1 158 1 MG MG . L 4 HOH A 1 159 1 HOH HOH . L 4 HOH A 2 160 5 HOH HOH . L 4 HOH A 3 161 15 HOH HOH . L 4 HOH A 4 162 17 HOH HOH . L 4 HOH A 5 163 21 HOH HOH . L 4 HOH A 6 164 25 HOH HOH . L 4 HOH A 7 165 33 HOH HOH . L 4 HOH A 8 166 34 HOH HOH . L 4 HOH A 9 167 36 HOH HOH . L 4 HOH A 10 168 41 HOH HOH . L 4 HOH A 11 169 47 HOH HOH . L 4 HOH A 12 170 49 HOH HOH . L 4 HOH A 13 171 51 HOH HOH . L 4 HOH A 14 172 52 HOH HOH . L 4 HOH A 15 173 55 HOH HOH . L 4 HOH A 16 174 62 HOH HOH . L 4 HOH A 17 175 78 HOH HOH . L 4 HOH A 18 176 81 HOH HOH . L 4 HOH A 19 177 91 HOH HOH . L 4 HOH A 20 178 178 HOH HOH . L 4 HOH A 21 179 93 HOH HOH . L 4 HOH A 22 180 104 HOH HOH . L 4 HOH A 23 181 107 HOH HOH . L 4 HOH A 24 182 108 HOH HOH . L 4 HOH A 25 183 126 HOH HOH . L 4 HOH A 26 184 184 HOH HOH . L 4 HOH A 27 185 128 HOH HOH . L 4 HOH A 28 186 149 HOH HOH . L 4 HOH A 29 190 190 HOH HOH . L 4 HOH A 30 198 198 HOH HOH . L 4 HOH A 31 203 203 HOH HOH . L 4 HOH A 32 207 207 HOH HOH . L 4 HOH A 33 223 223 HOH HOH . L 4 HOH A 34 228 228 HOH HOH . L 4 HOH A 35 230 230 HOH HOH . L 4 HOH A 36 236 236 HOH HOH . L 4 HOH A 37 243 243 HOH HOH . L 4 HOH A 38 245 245 HOH HOH . L 4 HOH A 39 251 251 HOH HOH . L 4 HOH A 40 255 255 HOH HOH . L 4 HOH A 41 256 256 HOH HOH . L 4 HOH A 42 257 257 HOH HOH . L 4 HOH A 43 259 259 HOH HOH . L 4 HOH A 44 270 270 HOH HOH . L 4 HOH A 45 271 271 HOH HOH . L 4 HOH A 46 272 272 HOH HOH . L 4 HOH A 47 274 274 HOH HOH . L 4 HOH A 48 275 275 HOH HOH . L 4 HOH A 49 276 276 HOH HOH . L 4 HOH A 50 277 277 HOH HOH . L 4 HOH A 51 278 278 HOH HOH . L 4 HOH A 52 279 279 HOH HOH . L 4 HOH A 53 283 283 HOH HOH . L 4 HOH A 54 284 284 HOH HOH . M 4 HOH B 1 158 4 HOH HOH . M 4 HOH B 2 159 6 HOH HOH . M 4 HOH B 3 160 12 HOH HOH . M 4 HOH B 4 161 13 HOH HOH . M 4 HOH B 5 162 14 HOH HOH . M 4 HOH B 6 163 22 HOH HOH . M 4 HOH B 7 164 28 HOH HOH . M 4 HOH B 8 165 37 HOH HOH . M 4 HOH B 9 166 38 HOH HOH . M 4 HOH B 10 167 50 HOH HOH . M 4 HOH B 11 168 168 HOH HOH . M 4 HOH B 12 169 59 HOH HOH . M 4 HOH B 13 170 66 HOH HOH . M 4 HOH B 14 171 86 HOH HOH . M 4 HOH B 15 172 87 HOH HOH . M 4 HOH B 16 173 88 HOH HOH . M 4 HOH B 17 174 100 HOH HOH . M 4 HOH B 18 175 105 HOH HOH . M 4 HOH B 19 176 113 HOH HOH . M 4 HOH B 20 177 114 HOH HOH . M 4 HOH B 21 178 117 HOH HOH . M 4 HOH B 22 179 125 HOH HOH . M 4 HOH B 23 180 140 HOH HOH . M 4 HOH B 24 181 142 HOH HOH . M 4 HOH B 25 191 191 HOH HOH . M 4 HOH B 26 209 209 HOH HOH . M 4 HOH B 27 237 237 HOH HOH . M 4 HOH B 28 254 254 HOH HOH . M 4 HOH B 29 263 263 HOH HOH . M 4 HOH B 30 264 264 HOH HOH . M 4 HOH B 31 281 281 HOH HOH . M 4 HOH B 32 285 285 HOH HOH . N 4 HOH C 1 159 159 HOH HOH . N 4 HOH C 2 160 2 HOH HOH . N 4 HOH C 3 161 3 HOH HOH . N 4 HOH C 4 162 16 HOH HOH . N 4 HOH C 5 163 19 HOH HOH . N 4 HOH C 6 164 20 HOH HOH . N 4 HOH C 7 165 23 HOH HOH . N 4 HOH C 8 166 24 HOH HOH . N 4 HOH C 9 167 26 HOH HOH . N 4 HOH C 10 168 39 HOH HOH . N 4 HOH C 11 169 45 HOH HOH . N 4 HOH C 12 170 56 HOH HOH . N 4 HOH C 13 171 70 HOH HOH . N 4 HOH C 14 172 72 HOH HOH . N 4 HOH C 15 173 76 HOH HOH . N 4 HOH C 16 174 77 HOH HOH . N 4 HOH C 17 175 99 HOH HOH . N 4 HOH C 18 176 110 HOH HOH . N 4 HOH C 19 177 119 HOH HOH . N 4 HOH C 20 178 134 HOH HOH . N 4 HOH C 21 179 179 HOH HOH . N 4 HOH C 22 180 144 HOH HOH . N 4 HOH C 23 181 146 HOH HOH . N 4 HOH C 24 182 151 HOH HOH . N 4 HOH C 25 183 158 HOH HOH . N 4 HOH C 26 196 196 HOH HOH . N 4 HOH C 27 197 197 HOH HOH . N 4 HOH C 28 210 210 HOH HOH . N 4 HOH C 29 220 220 HOH HOH . N 4 HOH C 30 222 222 HOH HOH . N 4 HOH C 31 229 229 HOH HOH . N 4 HOH C 32 233 233 HOH HOH . N 4 HOH C 33 234 234 HOH HOH . N 4 HOH C 34 235 235 HOH HOH . N 4 HOH C 35 242 242 HOH HOH . N 4 HOH C 36 248 248 HOH HOH . N 4 HOH C 37 249 249 HOH HOH . N 4 HOH C 38 250 250 HOH HOH . N 4 HOH C 39 258 258 HOH HOH . N 4 HOH C 40 267 267 HOH HOH . N 4 HOH C 41 268 268 HOH HOH . N 4 HOH C 42 273 273 HOH HOH . N 4 HOH C 43 286 286 HOH HOH . O 4 HOH D 1 159 7 HOH HOH . O 4 HOH D 2 160 8 HOH HOH . O 4 HOH D 3 161 9 HOH HOH . O 4 HOH D 4 162 10 HOH HOH . O 4 HOH D 5 163 29 HOH HOH . O 4 HOH D 6 164 31 HOH HOH . O 4 HOH D 7 165 35 HOH HOH . O 4 HOH D 8 166 46 HOH HOH . O 4 HOH D 9 167 74 HOH HOH . O 4 HOH D 10 168 80 HOH HOH . O 4 HOH D 11 169 82 HOH HOH . O 4 HOH D 12 170 90 HOH HOH . O 4 HOH D 13 171 106 HOH HOH . O 4 HOH D 14 172 109 HOH HOH . O 4 HOH D 15 173 111 HOH HOH . O 4 HOH D 16 174 130 HOH HOH . O 4 HOH D 17 175 143 HOH HOH . O 4 HOH D 18 176 150 HOH HOH . O 4 HOH D 19 177 152 HOH HOH . O 4 HOH D 20 199 199 HOH HOH . O 4 HOH D 21 215 215 HOH HOH . O 4 HOH D 22 216 216 HOH HOH . O 4 HOH D 23 226 226 HOH HOH . O 4 HOH D 24 227 227 HOH HOH . O 4 HOH D 25 231 231 HOH HOH . O 4 HOH D 26 239 239 HOH HOH . O 4 HOH D 27 247 247 HOH HOH . O 4 HOH D 28 252 252 HOH HOH . O 4 HOH D 29 253 253 HOH HOH . O 4 HOH D 30 261 261 HOH HOH . O 4 HOH D 31 265 265 HOH HOH . O 4 HOH D 32 266 266 HOH HOH . O 4 HOH D 33 269 269 HOH HOH . O 4 HOH D 34 287 287 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 APC . . . J 2 10.911 -70.593 -34.206 1 70.29 ? PG APC 200 D 1 HETATM 2 O O1G APC . . . J 2 11.265 -69.34 -33.426 1 71.97 ? O1G APC 200 D 1 HETATM 3 O O2G APC . . . J 2 9.926 -70.362 -35.336 1 69.73 ? O2G APC 200 D 1 HETATM 4 O O3G APC . . . J 2 10.638 -71.775 -33.319 1 69.6 ? O3G APC 200 D 1 HETATM 5 P PB APC . . . J 2 13.451 -70.156 -35.514 1 68.14 ? PB APC 200 D 1 HETATM 6 O O1B APC . . . J 2 14.599 -71.134 -35.682 1 66.49 ? O1B APC 200 D 1 HETATM 7 O O2B APC . . . J 2 12.875 -69.448 -36.732 1 67.6 ? O2B APC 200 D 1 HETATM 8 O O3B APC . . . J 2 12.256 -71.091 -34.952 1 69.71 ? O3B APC 200 D 1 HETATM 9 P PA APC . . . J 2 15.159 -67.743 -34.382 1 61.43 ? PA APC 200 D 1 HETATM 10 O O1A APC . . . J 2 16.34 -68.108 -33.546 1 60.42 ? O1A APC 200 D 1 HETATM 11 O O2A APC . . . J 2 14.489 -66.429 -34.06 1 63.22 ? O2A APC 200 D 1 HETATM 12 C C3A APC . . . J 2 13.876 -69.008 -34.156 1 64.74 ? C3A APC 200 D 1 HETATM 13 O O5' APC . . . J 2 15.661 -67.724 -35.914 1 60.91 ? O5' APC 200 D 1 HETATM 14 C C5' APC . . . J 2 16.626 -66.811 -36.44 1 59.68 ? C5' APC 200 D 1 HETATM 15 C C4' APC . . . J 2 16.331 -66.511 -37.917 1 60.61 ? C4' APC 200 D 1 HETATM 16 O O4' APC . . . J 2 16.804 -67.545 -38.812 1 59.74 ? O4' APC 200 D 1 HETATM 17 C C3' APC . . . J 2 14.832 -66.327 -38.167 1 60.56 ? C3' APC 200 D 1 HETATM 18 O O3' APC . . . J 2 14.59 -65.103 -38.876 1 61.29 ? O3' APC 200 D 1 HETATM 19 C C2' APC . . . J 2 14.434 -67.521 -39.015 1 60.07 ? C2' APC 200 D 1 HETATM 20 O O2' APC . . . J 2 13.418 -67.205 -39.979 1 62.39 ? O2' APC 200 D 1 HETATM 21 C C1' APC . . . J 2 15.733 -68.008 -39.667 1 58.09 ? C1' APC 200 D 1 HETATM 22 N N9 APC . . . J 2 15.649 -69.496 -39.862 1 54.68 ? N9 APC 200 D 1 HETATM 23 C C8 APC . . . J 2 15.265 -70.386 -38.932 1 53.73 ? C8 APC 200 D 1 HETATM 24 N N7 APC . . . J 2 15.277 -71.637 -39.435 1 50.67 ? N7 APC 200 D 1 HETATM 25 C C5 APC . . . J 2 15.669 -71.548 -40.71 1 50.8 ? C5 APC 200 D 1 HETATM 26 C C6 APC . . . J 2 15.847 -72.498 -41.712 1 48.87 ? C6 APC 200 D 1 HETATM 27 N N6 APC . . . J 2 15.629 -73.805 -41.471 1 48.95 ? N6 APC 200 D 1 HETATM 28 N N1 APC . . . J 2 16.248 -72.112 -42.931 1 47.56 ? N1 APC 200 D 1 HETATM 29 C C2 APC . . . J 2 16.467 -70.809 -43.18 1 50.22 ? C2 APC 200 D 1 HETATM 30 N N3 APC . . . J 2 16.3 -69.858 -42.241 1 52.31 ? N3 APC 200 D 1 HETATM 31 C C4 APC . . . J 2 15.895 -70.199 -40.983 1 52.97 ? C4 APC 200 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #