data_5ZK5 # _model_server_result.job_id x4_a2XOu1wHoSzZkxU3pIg _model_server_result.datetime_utc '2025-03-06 06:37:24' _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 5zk5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 5ZK5 # _exptl.entry_id 5ZK5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.223 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "7N-METHYL-8-HYDROGUANOSINE-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 5ZK5 _cell.length_a 37.48 _cell.length_b 65.09 _cell.length_c 76.39 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZK5 _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 _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 3 _struct_asym.id C _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 covale ? covale1 B C LEU 11 B LEU 11 1_555 B N MK8 12 B MK8 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale2 B C MK8 12 B MK8 12 1_555 B N PHE 13 B PHE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.292 ? covale ? covale3 B C ARG 15 B ARG 15 1_555 B N MK8 16 B MK8 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.365 ? covale ? covale4 B N NH2 17 B NH2 17 1_555 B C MK8 16 B MK8 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? # _chem_comp.formula 'C11 H20 N5 O14 P3' _chem_comp.formula_weight 539.223 _chem_comp.id MGT _chem_comp.mon_nstd_flag n _chem_comp.name "7N-METHYL-8-HYDROGUANOSINE-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 MGT doub 243 n n PG O2G MGT sing 244 n n PG O3G MGT sing 245 n n PG O3B MGT sing 246 n n O2G HOG2 MGT sing 247 n n O3G HOG3 MGT sing 248 n n O3B PB MGT sing 249 n n PB O1B MGT doub 250 n n PB O2B MGT sing 251 n n PB O3A MGT sing 252 n n O2B HOB2 MGT sing 253 n n O3A PA MGT sing 254 n n PA O1A MGT doub 255 n n PA O2A MGT sing 256 n n PA O5' MGT sing 257 n n O2A HOA2 MGT sing 258 n n O5' C5' MGT sing 259 n n C5' C4' MGT sing 260 n n C5' "H5'1" MGT sing 261 n n C5' "H5'2" MGT sing 262 n n C4' O4' MGT sing 263 n n C4' C3' MGT sing 264 n n C4' H4' MGT sing 265 n n O4' C1' MGT sing 266 n n C3' O3' MGT sing 267 n n C3' C2' MGT sing 268 n n C3' H3' MGT sing 269 n n O3' HO3' MGT sing 270 n n C2' O2' MGT sing 271 n n C2' C1' MGT sing 272 n n C2' H2' MGT sing 273 n n O2' HO2' MGT sing 274 n n C1' N9 MGT sing 275 n n C1' H1' MGT sing 276 n n N9 C8 MGT sing 277 n n N9 C4 MGT sing 278 n n C8 N7 MGT sing 279 n n C8 H81 MGT sing 280 n n C8 H82 MGT sing 281 n n N7 CM7 MGT sing 282 n n N7 C5 MGT sing 283 n n CM7 HM71 MGT sing 284 n n CM7 HM72 MGT sing 285 n n CM7 HM73 MGT sing 286 n n C5 C6 MGT sing 287 n n C5 C4 MGT doub 288 n n C6 O6 MGT doub 289 n n C6 N1 MGT sing 290 n n N1 C2 MGT sing 291 n n N1 HN1 MGT sing 292 n n C2 N2 MGT sing 293 n n C2 N3 MGT doub 294 n n N2 HN21 MGT sing 295 n n N2 HN22 MGT sing 296 n n N3 C4 MGT sing 297 n n # _atom_sites.entry_id 5ZK5 _atom_sites.fract_transf_matrix[1][1] 0.026681 _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] 0.015363 _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] 0.013091 _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 MGT A 1 1001 1001 MGT MGT . D 4 HOH A 1 1101 11 HOH HOH . D 4 HOH A 2 1102 15 HOH HOH . D 4 HOH A 3 1103 36 HOH HOH . D 4 HOH A 4 1104 19 HOH HOH . D 4 HOH A 5 1105 18 HOH HOH . D 4 HOH A 6 1106 2 HOH HOH . D 4 HOH A 7 1107 37 HOH HOH . D 4 HOH A 8 1108 52 HOH HOH . D 4 HOH A 9 1109 25 HOH HOH . D 4 HOH A 10 1110 49 HOH HOH . D 4 HOH A 11 1111 28 HOH HOH . D 4 HOH A 12 1112 1 HOH HOH . D 4 HOH A 13 1113 14 HOH HOH . D 4 HOH A 14 1114 40 HOH HOH . D 4 HOH A 15 1115 24 HOH HOH . D 4 HOH A 16 1116 45 HOH HOH . D 4 HOH A 17 1117 21 HOH HOH . D 4 HOH A 18 1118 44 HOH HOH . D 4 HOH A 19 1119 23 HOH HOH . D 4 HOH A 20 1120 12 HOH HOH . D 4 HOH A 21 1121 7 HOH HOH . D 4 HOH A 22 1122 17 HOH HOH . D 4 HOH A 23 1123 32 HOH HOH . D 4 HOH A 24 1124 43 HOH HOH . D 4 HOH A 25 1125 47 HOH HOH . D 4 HOH A 26 1126 33 HOH HOH . D 4 HOH A 27 1127 6 HOH HOH . D 4 HOH A 28 1128 42 HOH HOH . D 4 HOH A 29 1129 39 HOH HOH . D 4 HOH A 30 1130 46 HOH HOH . D 4 HOH A 31 1131 20 HOH HOH . D 4 HOH A 32 1132 41 HOH HOH . D 4 HOH A 33 1133 5 HOH HOH . D 4 HOH A 34 1134 4 HOH HOH . D 4 HOH A 35 1135 10 HOH HOH . D 4 HOH A 36 1136 27 HOH HOH . D 4 HOH A 37 1137 13 HOH HOH . D 4 HOH A 38 1138 55 HOH HOH . D 4 HOH A 39 1139 26 HOH HOH . D 4 HOH A 40 1140 53 HOH HOH . D 4 HOH A 41 1141 34 HOH HOH . D 4 HOH A 42 1142 48 HOH HOH . D 4 HOH A 43 1143 54 HOH HOH . D 4 HOH A 44 1144 56 HOH HOH . D 4 HOH A 45 1145 50 HOH HOH . D 4 HOH A 46 1146 16 HOH HOH . D 4 HOH A 47 1147 35 HOH HOH . D 4 HOH A 48 1148 3 HOH HOH . D 4 HOH A 49 1149 51 HOH HOH . D 4 HOH A 50 1150 9 HOH HOH . D 4 HOH A 51 1151 38 HOH HOH . D 4 HOH A 52 1152 31 HOH HOH . D 4 HOH A 53 1153 22 HOH HOH . E 4 HOH B 1 201 8 HOH HOH . E 4 HOH B 2 202 30 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 MGT . . . C 3 34.057 51.813 81.004 1 69.34 ? PG MGT 1001 A 1 HETATM 2 O O1G MGT . . . C 3 35.261 52.109 81.877 1 63.63 ? O1G MGT 1001 A 1 HETATM 3 O O2G MGT . . . C 3 32.742 52.279 81.604 1 65.36 ? O2G MGT 1001 A 1 HETATM 4 O O3G MGT . . . C 3 34.028 50.378 80.525 1 67.36 ? O3G MGT 1001 A 1 HETATM 5 O O3B MGT . . . C 3 34.219 52.671 79.625 1 55.97 ? O3B MGT 1001 A 1 HETATM 6 P PB MGT . . . C 3 34.565 54.239 79.576 1 50.4 ? PB MGT 1001 A 1 HETATM 7 O O1B MGT . . . C 3 34.599 54.744 78.152 1 52.48 ? O1B MGT 1001 A 1 HETATM 8 O O2B MGT . . . C 3 33.662 54.95 80.536 1 49.82 ? O2B MGT 1001 A 1 HETATM 9 O O3A MGT . . . C 3 36.044 54.293 80.235 1 49.65 ? O3A MGT 1001 A 1 HETATM 10 P PA MGT . . . C 3 37.449 54.493 79.47 1 46.9 ? PA MGT 1001 A 1 HETATM 11 O O1A MGT . . . C 3 37.299 55.343 78.226 1 48.29 ? O1A MGT 1001 A 1 HETATM 12 O O2A MGT . . . C 3 38.534 54.822 80.466 1 43.88 ? O2A MGT 1001 A 1 HETATM 13 O O5' MGT . . . C 3 37.813 53.012 79.004 1 49.08 ? O5' MGT 1001 A 1 HETATM 14 C C5' MGT . . . C 3 37.018 52.236 78.129 1 47.47 ? C5' MGT 1001 A 1 HETATM 15 C C4' MGT . . . C 3 37.952 51.324 77.366 1 45.74 ? C4' MGT 1001 A 1 HETATM 16 O O4' MGT . . . C 3 38.98 52.051 76.68 1 44.56 ? O4' MGT 1001 A 1 HETATM 17 C C3' MGT . . . C 3 38.652 50.353 78.318 1 45.73 ? C3' MGT 1001 A 1 HETATM 18 O O3' MGT . . . C 3 37.859 49.198 78.61 1 43.33 ? O3' MGT 1001 A 1 HETATM 19 C C2' MGT . . . C 3 39.946 50.054 77.591 1 44.28 ? C2' MGT 1001 A 1 HETATM 20 O O2' MGT . . . C 3 39.835 48.94 76.725 1 48.91 ? O2' MGT 1001 A 1 HETATM 21 C C1' MGT . . . C 3 40.21 51.312 76.775 1 44.02 ? C1' MGT 1001 A 1 HETATM 22 N N9 MGT . . . C 3 41.289 52.034 77.5 1 42.12 ? N9 MGT 1001 A 1 HETATM 23 C C8 MGT . . . C 3 40.888 53.127 78.396 1 42.09 ? C8 MGT 1001 A 1 HETATM 24 N N7 MGT . . . C 3 42.231 53.486 78.848 1 40.34 ? N7 MGT 1001 A 1 HETATM 25 C CM7 MGT . . . C 3 42.225 54.614 79.812 1 40.4 ? CM7 MGT 1001 A 1 HETATM 26 C C5 MGT . . . C 3 43.212 52.741 78.347 1 38.2 ? C5 MGT 1001 A 1 HETATM 27 C C6 MGT . . . C 3 44.674 52.714 78.52 1 36.16 ? C6 MGT 1001 A 1 HETATM 28 O O6 MGT . . . C 3 45.3 53.493 79.258 1 33.73 ? O6 MGT 1001 A 1 HETATM 29 N N1 MGT . . . C 3 45.32 51.787 77.82 1 38.2 ? N1 MGT 1001 A 1 HETATM 30 C C2 MGT . . . C 3 44.686 50.911 77.006 1 38.69 ? C2 MGT 1001 A 1 HETATM 31 N N2 MGT . . . C 3 45.4 50.004 76.33 1 38.08 ? N2 MGT 1001 A 1 HETATM 32 N N3 MGT . . . C 3 43.344 50.87 76.807 1 39.11 ? N3 MGT 1001 A 1 HETATM 33 C C4 MGT . . . C 3 42.577 51.756 77.447 1 39.54 ? C4 MGT 1001 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #