data_7YZI # _model_server_result.job_id '_NEg0UY5NO1kLYHqOvb2eg' _model_server_result.datetime_utc '2024-11-28 14:46:44' _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 7yzi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 7YZI # _exptl.entry_id 7YZI _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 656.328 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-O-(N-METHYLANTHRANILOYL)-GUANOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 7YZI _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YZI _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 I 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 disulf ? disulf1 C SG CYS 24 C CYS 27 1_555 C SG CYS 97 C CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf2 D SG CYS 24 D CYS 27 1_555 D SG CYS 97 D CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf3 E SG CYS 24 E CYS 27 1_555 E SG CYS 97 E CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc1 A OD2 ASP 282 A ASP 256 1_555 G MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc2 A OD1 ASP 282 A ASP 256 1_555 H MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc3 A O ILE 283 A ILE 257 1_555 G MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc4 A OD2 ASP 326 A ASP 300 1_555 G MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc5 A OD1 ASP 326 A ASP 300 1_555 H MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc6 A OD2 ASP 326 A ASP 300 1_555 H MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc7 F PB ONM . A ONM 501 1_555 G MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc8 F O1B ONM . A ONM 501 1_555 G MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc9 F O2G ONM . A ONM 501 1_555 G MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc10 F O3G ONM . A ONM 501 1_555 G MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc11 F O2A ONM . A ONM 501 1_555 H MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? metalc ? metalc12 B OD2 ASP 282 B ASP 256 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc13 B OD1 ASP 282 B ASP 256 1_555 K MN MN . B MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc14 B O ILE 283 B ILE 257 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc15 B OD2 ASP 326 B ASP 300 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc16 B OD1 ASP 326 B ASP 300 1_555 K MN MN . B MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc17 B OD2 ASP 326 B ASP 300 1_555 K MN MN . B MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc18 I PB ONM . B ONM 501 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc19 I O1B ONM . B ONM 501 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc20 I O2G ONM . B ONM 501 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc21 I O3G ONM . B ONM 501 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc22 I O2A ONM . B ONM 501 1_555 K MN MN . B MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? # _chem_comp.formula 'C18 H23 N6 O15 P3' _chem_comp.formula_weight 656.328 _chem_comp.id ONM _chem_comp.mon_nstd_flag . _chem_comp.name "3'-O-(N-METHYLANTHRANILOYL)-GUANOSINE-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 CA7 NA1 ONM sing 235 n n CA7 HA71 ONM sing 236 n n CA7 HA72 ONM sing 237 n n CA7 HA73 ONM sing 238 n n NA1 CA6 ONM sing 239 n n NA1 HA1 ONM sing 240 n n CA6 CA5 ONM doub 241 n y CA6 CA1 ONM sing 242 n y CA5 CA4 ONM sing 243 n y CA5 HA5 ONM sing 244 n n CA4 CA3 ONM doub 245 n y CA4 HA4 ONM sing 246 n n CA3 CA2 ONM sing 247 n y CA3 HA3 ONM sing 248 n n CA2 CA1 ONM doub 249 n y CA2 HA2 ONM sing 250 n n CA1 CA ONM sing 251 n n CA OA ONM doub 252 n n CA O3' ONM sing 253 n n O3' C3' ONM sing 254 n n C3' C2' ONM sing 255 n n C3' C4' ONM sing 256 n n C3' H3' ONM sing 257 n n C2' O2' ONM sing 258 n n C2' C1' ONM sing 259 n n C2' H1 ONM sing 260 n n O2' H2' ONM sing 261 n n C4' C5' ONM sing 262 n n C4' O4' ONM sing 263 n n C4' H4' ONM sing 264 n n C5' O5' ONM sing 265 n n C5' "H5'1" ONM sing 266 n n C5' "H5'2" ONM sing 267 n n O5' PA ONM sing 268 n n PA O3A ONM doub 269 n n PA O2A ONM sing 270 n n PA O1A ONM sing 271 n n O2A H2A ONM sing 272 n n O1A PB ONM sing 273 n n PB O3B ONM doub 274 n n PB O2B ONM sing 275 n n PB O1B ONM sing 276 n n O2B H2B ONM sing 277 n n O1B PG ONM sing 278 n n PG O2G ONM doub 279 n n PG O3G ONM sing 280 n n PG O1G ONM sing 281 n n O3G H3G ONM sing 282 n n O1G H1G ONM sing 283 n n O4' C1' ONM sing 284 n n C1' N9 ONM sing 285 n n C1' H1' ONM sing 286 n n N9 C8 ONM sing 287 n y N9 C4 ONM sing 288 n y C8 N7 ONM doub 289 n y C8 H8 ONM sing 290 n n N7 C5 ONM sing 291 n y C5 C4 ONM doub 292 n y C5 C6 ONM sing 293 n n C4 N3 ONM sing 294 n n N3 C2 ONM doub 295 n n C2 N2 ONM sing 296 n n C2 N1 ONM sing 297 n n N2 HN21 ONM sing 298 n n N2 HN22 ONM sing 299 n n N1 C6 ONM sing 300 n n N1 HN1 ONM sing 301 n n C6 O6 ONM doub 302 n n # _atom_sites.entry_id 7YZI _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 3 ONM A 1 501 429 ONM ONM . G 4 MN A 1 502 431 MN MN . H 4 MN A 1 503 432 MN MN . I 3 ONM B 1 501 429 ONM ONM . J 4 MN B 1 502 431 MN MN . K 4 MN B 1 503 432 MN MN . # 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 C CA7 ONM . . . I 3 118.882 120.472 69.342 1 75.74 ? CA7 ONM 501 B 1 HETATM 2 N NA1 ONM . . . I 3 120.095 121.278 69.635 1 75.74 ? NA1 ONM 501 B 1 HETATM 3 C CA6 ONM . . . I 3 120.796 121.077 70.861 1 75.74 ? CA6 ONM 501 B 1 HETATM 4 C CA5 ONM . . . I 3 120.223 120.318 71.86 1 75.74 ? CA5 ONM 501 B 1 HETATM 5 C CA4 ONM . . . I 3 120.892 120.115 73.05 1 75.74 ? CA4 ONM 501 B 1 HETATM 6 C CA3 ONM . . . I 3 122.143 120.673 73.243 1 75.74 ? CA3 ONM 501 B 1 HETATM 7 C CA2 ONM . . . I 3 122.718 121.43 72.244 1 75.74 ? CA2 ONM 501 B 1 HETATM 8 C CA1 ONM . . . I 3 122.051 121.636 71.054 1 75.74 ? CA1 ONM 501 B 1 HETATM 9 C CA ONM . . . I 3 122.749 122.513 69.938 1 75.74 ? CA ONM 501 B 1 HETATM 10 O OA ONM . . . I 3 122.189 122.744 68.91 1 75.74 ? OA ONM 501 B 1 HETATM 11 O O3' ONM . . . I 3 124.066 123.012 70.201 1 75.74 ? O3' ONM 501 B 1 HETATM 12 C C3' ONM . . . I 3 124.643 123.797 69.244 1 75.74 ? C3' ONM 501 B 1 HETATM 13 C C2' ONM . . . I 3 124.533 125.234 69.633 1 75.74 ? C2' ONM 501 B 1 HETATM 14 O O2' ONM . . . I 3 123.221 125.515 70.296 1 75.74 ? O2' ONM 501 B 1 HETATM 15 C C4' ONM . . . I 3 126.213 123.543 69.219 1 75.74 ? C4' ONM 501 B 1 HETATM 16 C C5' ONM . . . I 3 126.735 123.459 67.763 1 75.74 ? C5' ONM 501 B 1 HETATM 17 O O5' ONM . . . I 3 126.536 124.689 67.109 1 75.74 ? O5' ONM 501 B 1 HETATM 18 P PA ONM . . . I 3 127.825 125.357 66.353 1 75.74 ? PA ONM 501 B 1 HETATM 19 O O3A ONM . . . I 3 127.51 126.796 66.018 1 75.74 ? O3A ONM 501 B 1 HETATM 20 O O2A ONM . . . I 3 129.029 125.294 67.252 1 75.74 ? O2A ONM 501 B 1 HETATM 21 O O1A ONM . . . I 3 128.146 124.52 64.949 1 75.74 ? O1A ONM 501 B 1 HETATM 22 P PB ONM . . . I 3 128.219 122.877 64.83 1 75.74 ? PB ONM 501 B 1 HETATM 23 O O3B ONM . . . I 3 129.028 122.308 65.966 1 75.74 ? O3B ONM 501 B 1 HETATM 24 O O2B ONM . . . I 3 126.834 122.297 64.861 1 75.74 ? O2B ONM 501 B 1 HETATM 25 O O1B ONM . . . I 3 128.957 122.488 63.412 1 75.74 ? O1B ONM 501 B 1 HETATM 26 P PG ONM . . . I 3 130.425 123.13 63.011 0.45 75.74 ? PG ONM 501 B 1 HETATM 27 O O2G ONM . . . I 3 131.48 122.053 63.071 1 75.74 ? O2G ONM 501 B 1 HETATM 28 O O3G ONM . . . I 3 130.765 124.224 64.012 1 75.74 ? O3G ONM 501 B 1 HETATM 29 O O1G ONM . . . I 3 130.363 123.719 61.616 1 75.74 ? O1G ONM 501 B 1 HETATM 30 O O4' ONM . . . I 3 126.749 124.556 69.807 1 75.74 ? O4' ONM 501 B 1 HETATM 31 C C1' ONM . . . I 3 125.532 125.351 70.503 1 75.74 ? C1' ONM 501 B 1 HETATM 32 N N9 ONM . . . I 3 125.882 126.717 70.733 1 75.74 ? N9 ONM 501 B 1 HETATM 33 C C8 ONM . . . I 3 126.52 127.515 69.859 1 75.74 ? C8 ONM 501 B 1 HETATM 34 N N7 ONM . . . I 3 126.676 128.728 70.436 1 75.74 ? N7 ONM 501 B 1 HETATM 35 C C5 ONM . . . I 3 126.143 128.671 71.65 1 75.74 ? C5 ONM 501 B 1 HETATM 36 C C4 ONM . . . I 3 125.65 127.417 71.834 1 75.74 ? C4 ONM 501 B 1 HETATM 37 N N3 ONM . . . I 3 124.981 127.032 73.115 1 75.74 ? N3 ONM 501 B 1 HETATM 38 C C2 ONM . . . I 3 124.855 128.018 74.183 1 75.74 ? C2 ONM 501 B 1 HETATM 39 N N2 ONM . . . I 3 124.205 127.654 75.432 1 75.74 ? N2 ONM 501 B 1 HETATM 40 N N1 ONM . . . I 3 125.372 129.351 74.002 1 75.74 ? N1 ONM 501 B 1 HETATM 41 C C6 ONM . . . I 3 126.011 129.711 72.774 1 75.74 ? C6 ONM 501 B 1 HETATM 42 O O6 ONM . . . I 3 126.438 130.808 72.622 1 75.74 ? O6 ONM 501 B 1 HETATM 43 H HA71 ONM . . . I 3 118.188 120.693 69.983 1 75.73 ? HA71 ONM 501 B 1 HETATM 44 H HA72 ONM . . . I 3 118.569 120.668 68.445 1 75.73 ? HA72 ONM 501 B 1 HETATM 45 H HA73 ONM . . . I 3 119.095 119.529 69.414 1 75.73 ? HA73 ONM 501 B 1 HETATM 46 H HA1 ONM . . . I 3 120.373 121.863 69.07 1 75.73 ? HA1 ONM 501 B 1 HETATM 47 H HA5 ONM . . . I 3 119.384 119.941 71.734 1 75.73 ? HA5 ONM 501 B 1 HETATM 48 H HA4 ONM . . . I 3 120.503 119.604 73.72 1 75.73 ? HA4 ONM 501 B 1 HETATM 49 H HA3 ONM . . . I 3 122.595 120.538 74.044 1 75.73 ? HA3 ONM 501 B 1 HETATM 50 H HA2 ONM . . . I 3 123.557 121.807 72.373 1 75.73 ? HA2 ONM 501 B 1 HETATM 51 H H3' ONM . . . I 3 124.257 123.646 68.37 1 75.73 ? H3' ONM 501 B 1 HETATM 52 H H1 ONM . . . I 3 124.674 125.804 68.863 1 75.73 ? H1 ONM 501 B 1 HETATM 53 H H2' ONM . . . I 3 123.209 126.325 70.554 1 75.73 ? H2' ONM 501 B 1 HETATM 54 H H4' ONM . . . I 3 126.42 122.731 69.703 1 75.73 ? H4' ONM 501 B 1 HETATM 55 H "H5'1" ONM . . . I 3 127.683 123.253 67.768 1 75.73 ? "H5'1" ONM 501 B 1 HETATM 56 H "H5'2" ONM . . . I 3 126.256 122.764 67.29 1 75.73 ? "H5'2" ONM 501 B 1 HETATM 57 H H1' ONM . . . I 3 125.288 124.921 71.336 1 75.73 ? H1' ONM 501 B 1 HETATM 58 H H8 ONM . . . I 3 126.802 127.275 69.006 1 75.73 ? H8 ONM 501 B 1 HETATM 59 H HN21 ONM . . . I 3 123.901 126.858 75.533 1 75.73 ? HN21 ONM 501 B 1 HETATM 60 H HN22 ONM . . . I 3 124.127 128.232 76.065 1 75.73 ? HN22 ONM 501 B 1 HETATM 61 H HN1 ONM . . . I 3 125.289 129.923 74.629 1 75.73 ? HN1 ONM 501 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 61 #