data_5ZK7 # _model_server_result.job_id BDljtus6gN_HCifK-XDM3Q _model_server_result.datetime_utc '2024-11-19 14:31:15' _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 5zk7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1001}' # _entry.id 5ZK7 # _exptl.entry_id 5ZK7 _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 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 5ZK7 _cell.length_a 57.35 _cell.length_b 68.17 _cell.length_c 111.01 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZK7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,D,E,F,G,H,I,L,M,N,Q 1 1 B,C,J,K,O,P 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 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 covale ? covale1 C C ACE 1 C ACE 0 1_555 C N ARG 2 C ARG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale2 C C ARG 5 C ARG 4 1_555 C N MK8 6 C MK8 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale3 C C MK8 6 C MK8 5 1_555 C N GLN 7 C GLN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.277 ? covale ? covale4 C C LEU 9 C LEU 8 1_555 C N MK8 10 C MK8 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale5 C C MK8 10 C MK8 9 1_555 C N LEU 11 C LEU 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.288 ? covale ? covale6 C C ARG 13 C ARG 12 1_555 C N NH2 14 C NH2 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale7 D C ACE 1 D ACE 0 1_555 D N ARG 2 D ARG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 ? covale ? covale8 D C ARG 5 D ARG 4 1_555 D N MK8 6 D MK8 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? covale ? covale9 D C MK8 6 D MK8 5 1_555 D N GLN 7 D GLN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.279 ? covale ? covale10 D C LEU 9 D LEU 8 1_555 D N MK8 10 D MK8 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale11 D C MK8 10 D MK8 9 1_555 D N LEU 11 D LEU 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.273 ? covale ? covale12 D C ARG 13 D ARG 12 1_555 D N NH2 14 D NH2 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? # _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 256 n n PG O2G MGT sing 257 n n PG O3G MGT sing 258 n n PG O3B MGT sing 259 n n O2G HOG2 MGT sing 260 n n O3G HOG3 MGT sing 261 n n O3B PB MGT sing 262 n n PB O1B MGT doub 263 n n PB O2B MGT sing 264 n n PB O3A MGT sing 265 n n O2B HOB2 MGT sing 266 n n O3A PA MGT sing 267 n n PA O1A MGT doub 268 n n PA O2A MGT sing 269 n n PA O5' MGT sing 270 n n O2A HOA2 MGT sing 271 n n O5' C5' MGT sing 272 n n C5' C4' MGT sing 273 n n C5' "H5'1" MGT sing 274 n n C5' "H5'2" MGT sing 275 n n C4' O4' MGT sing 276 n n C4' C3' MGT sing 277 n n C4' H4' MGT sing 278 n n O4' C1' MGT sing 279 n n C3' O3' MGT sing 280 n n C3' C2' MGT sing 281 n n C3' H3' MGT sing 282 n n O3' HO3' MGT sing 283 n n C2' O2' MGT sing 284 n n C2' C1' MGT sing 285 n n C2' H2' MGT sing 286 n n O2' HO2' MGT sing 287 n n C1' N9 MGT sing 288 n n C1' H1' MGT sing 289 n n N9 C8 MGT sing 290 n n N9 C4 MGT sing 291 n n C8 N7 MGT sing 292 n n C8 H81 MGT sing 293 n n C8 H82 MGT sing 294 n n N7 CM7 MGT sing 295 n n N7 C5 MGT sing 296 n n CM7 HM71 MGT sing 297 n n CM7 HM72 MGT sing 298 n n CM7 HM73 MGT sing 299 n n C5 C6 MGT sing 300 n n C5 C4 MGT doub 301 n n C6 O6 MGT doub 302 n n C6 N1 MGT sing 303 n n N1 C2 MGT sing 304 n n N1 HN1 MGT sing 305 n n C2 N2 MGT sing 306 n n C2 N3 MGT doub 307 n n N2 HN21 MGT sing 308 n n N2 HN22 MGT sing 309 n n N3 C4 MGT sing 310 n n # _atom_sites.entry_id 5ZK7 _atom_sites.fract_transf_matrix[1][1] 0.017437 _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] 0.014669 _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] 0.009008 _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 3 MGT A 1 1001 1001 MGT MGT . F 4 IOD A 1 1002 2 IOD IOD . G 4 IOD A 1 1003 3 IOD IOD . H 5 GOL A 1 1004 1 GOL GOL . I 6 CL A 1 1005 6 CL CL . J 3 MGT B 1 1001 1001 MGT MGT . K 4 IOD C 1 101 4 IOD IOD . L 4 IOD D 1 101 1 IOD IOD . M 4 IOD D 1 102 5 IOD IOD . N 7 HOH A 1 1101 131 HOH HOH . N 7 HOH A 2 1102 153 HOH HOH . N 7 HOH A 3 1103 43 HOH HOH . N 7 HOH A 4 1104 34 HOH HOH . N 7 HOH A 5 1105 25 HOH HOH . N 7 HOH A 6 1106 101 HOH HOH . N 7 HOH A 7 1107 105 HOH HOH . N 7 HOH A 8 1108 79 HOH HOH . N 7 HOH A 9 1109 83 HOH HOH . N 7 HOH A 10 1110 2 HOH HOH . N 7 HOH A 11 1111 77 HOH HOH . N 7 HOH A 12 1112 108 HOH HOH . N 7 HOH A 13 1113 71 HOH HOH . N 7 HOH A 14 1114 3 HOH HOH . N 7 HOH A 15 1115 47 HOH HOH . N 7 HOH A 16 1116 60 HOH HOH . N 7 HOH A 17 1117 82 HOH HOH . N 7 HOH A 18 1118 50 HOH HOH . N 7 HOH A 19 1119 141 HOH HOH . N 7 HOH A 20 1120 51 HOH HOH . N 7 HOH A 21 1121 150 HOH HOH . N 7 HOH A 22 1122 48 HOH HOH . N 7 HOH A 23 1123 35 HOH HOH . N 7 HOH A 24 1124 132 HOH HOH . N 7 HOH A 25 1125 4 HOH HOH . N 7 HOH A 26 1126 129 HOH HOH . N 7 HOH A 27 1127 10 HOH HOH . N 7 HOH A 28 1128 143 HOH HOH . N 7 HOH A 29 1129 32 HOH HOH . N 7 HOH A 30 1130 81 HOH HOH . N 7 HOH A 31 1131 54 HOH HOH . N 7 HOH A 32 1132 70 HOH HOH . N 7 HOH A 33 1133 17 HOH HOH . N 7 HOH A 34 1134 49 HOH HOH . N 7 HOH A 35 1135 9 HOH HOH . N 7 HOH A 36 1136 106 HOH HOH . N 7 HOH A 37 1137 80 HOH HOH . N 7 HOH A 38 1138 100 HOH HOH . N 7 HOH A 39 1139 151 HOH HOH . N 7 HOH A 40 1140 6 HOH HOH . N 7 HOH A 41 1141 128 HOH HOH . N 7 HOH A 42 1142 107 HOH HOH . N 7 HOH A 43 1143 57 HOH HOH . N 7 HOH A 44 1144 40 HOH HOH . N 7 HOH A 45 1145 104 HOH HOH . N 7 HOH A 46 1146 73 HOH HOH . N 7 HOH A 47 1147 78 HOH HOH . N 7 HOH A 48 1148 46 HOH HOH . N 7 HOH A 49 1149 5 HOH HOH . N 7 HOH A 50 1150 126 HOH HOH . N 7 HOH A 51 1151 68 HOH HOH . N 7 HOH A 52 1152 45 HOH HOH . N 7 HOH A 53 1153 27 HOH HOH . N 7 HOH A 54 1154 52 HOH HOH . N 7 HOH A 55 1155 84 HOH HOH . N 7 HOH A 56 1156 41 HOH HOH . N 7 HOH A 57 1157 152 HOH HOH . N 7 HOH A 58 1158 44 HOH HOH . N 7 HOH A 59 1159 134 HOH HOH . O 7 HOH B 1 1101 111 HOH HOH . O 7 HOH B 2 1102 113 HOH HOH . O 7 HOH B 3 1103 116 HOH HOH . O 7 HOH B 4 1104 94 HOH HOH . O 7 HOH B 5 1105 97 HOH HOH . O 7 HOH B 6 1106 91 HOH HOH . O 7 HOH B 7 1107 31 HOH HOH . O 7 HOH B 8 1108 95 HOH HOH . O 7 HOH B 9 1109 37 HOH HOH . O 7 HOH B 10 1110 123 HOH HOH . O 7 HOH B 11 1111 74 HOH HOH . O 7 HOH B 12 1112 85 HOH HOH . O 7 HOH B 13 1113 98 HOH HOH . O 7 HOH B 14 1114 56 HOH HOH . O 7 HOH B 15 1115 114 HOH HOH . O 7 HOH B 16 1116 23 HOH HOH . O 7 HOH B 17 1117 62 HOH HOH . O 7 HOH B 18 1118 92 HOH HOH . O 7 HOH B 19 1119 99 HOH HOH . O 7 HOH B 20 1120 90 HOH HOH . O 7 HOH B 21 1121 12 HOH HOH . O 7 HOH B 22 1122 11 HOH HOH . O 7 HOH B 23 1123 7 HOH HOH . O 7 HOH B 24 1124 8 HOH HOH . O 7 HOH B 25 1125 75 HOH HOH . O 7 HOH B 26 1126 89 HOH HOH . O 7 HOH B 27 1127 76 HOH HOH . O 7 HOH B 28 1128 118 HOH HOH . O 7 HOH B 29 1129 96 HOH HOH . O 7 HOH B 30 1130 140 HOH HOH . O 7 HOH B 31 1131 72 HOH HOH . O 7 HOH B 32 1132 109 HOH HOH . O 7 HOH B 33 1133 13 HOH HOH . O 7 HOH B 34 1134 139 HOH HOH . O 7 HOH B 35 1135 63 HOH HOH . O 7 HOH B 36 1136 148 HOH HOH . O 7 HOH B 37 1137 154 HOH HOH . O 7 HOH B 38 1138 155 HOH HOH . O 7 HOH B 39 1139 61 HOH HOH . O 7 HOH B 40 1140 124 HOH HOH . O 7 HOH B 41 1141 125 HOH HOH . O 7 HOH B 42 1142 38 HOH HOH . O 7 HOH B 43 1143 29 HOH HOH . O 7 HOH B 44 1144 53 HOH HOH . O 7 HOH B 45 1145 112 HOH HOH . O 7 HOH B 46 1146 138 HOH HOH . O 7 HOH B 47 1147 110 HOH HOH . O 7 HOH B 48 1148 30 HOH HOH . O 7 HOH B 49 1149 93 HOH HOH . O 7 HOH B 50 1150 36 HOH HOH . O 7 HOH B 51 1151 42 HOH HOH . O 7 HOH B 52 1152 69 HOH HOH . O 7 HOH B 53 1153 28 HOH HOH . P 7 HOH C 1 201 119 HOH HOH . P 7 HOH C 2 202 144 HOH HOH . P 7 HOH C 3 203 1 HOH HOH . P 7 HOH C 4 204 24 HOH HOH . P 7 HOH C 5 205 146 HOH HOH . P 7 HOH C 6 206 58 HOH HOH . P 7 HOH C 7 207 14 HOH HOH . P 7 HOH C 8 208 142 HOH HOH . Q 7 HOH D 1 201 16 HOH HOH . Q 7 HOH D 2 202 66 HOH HOH . Q 7 HOH D 3 203 26 HOH HOH . Q 7 HOH D 4 204 39 HOH HOH . Q 7 HOH D 5 205 127 HOH HOH . Q 7 HOH D 6 206 147 HOH HOH . Q 7 HOH D 7 207 59 HOH HOH . Q 7 HOH D 8 208 33 HOH HOH . Q 7 HOH D 9 209 130 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 O O3A MGT . . . J 3 -18.304 16.268 -33.168 1 64.39 ? O3A MGT 1001 B 1 HETATM 2 P PA MGT . . . J 3 -16.984 16.956 -33.425 1 63.4 ? PA MGT 1001 B 1 HETATM 3 O O1A MGT . . . J 3 -15.806 15.866 -33.251 1 64.25 ? O1A MGT 1001 B 1 HETATM 4 O O2A MGT . . . J 3 -16.626 18.216 -32.671 1 59.77 ? O2A MGT 1001 B 1 HETATM 5 O O5' MGT . . . J 3 -16.912 17.345 -34.984 1 62.13 ? O5' MGT 1001 B 1 HETATM 6 C C5' MGT . . . J 3 -16.518 16.429 -35.999 1 60.77 ? C5' MGT 1001 B 1 HETATM 7 C C4' MGT . . . J 3 -17.212 16.775 -37.313 1 60.34 ? C4' MGT 1001 B 1 HETATM 8 O O4' MGT . . . J 3 -18.623 16.561 -37.209 1 59.22 ? O4' MGT 1001 B 1 HETATM 9 C C3' MGT . . . J 3 -17.027 18.222 -37.758 1 59.28 ? C3' MGT 1001 B 1 HETATM 10 O O3' MGT . . . J 3 -15.867 18.366 -38.58 1 61.38 ? O3' MGT 1001 B 1 HETATM 11 C C2' MGT . . . J 3 -18.315 18.538 -38.492 1 59.13 ? C2' MGT 1001 B 1 HETATM 12 O O2' MGT . . . J 3 -18.198 18.286 -39.897 1 59.65 ? O2' MGT 1001 B 1 HETATM 13 C C1' MGT . . . J 3 -19.35 17.603 -37.875 1 58.12 ? C1' MGT 1001 B 1 HETATM 14 N N9 MGT . . . J 3 -20.238 18.38 -36.959 1 57.14 ? N9 MGT 1001 B 1 HETATM 15 C C8 MGT . . . J 3 -19.896 18.335 -35.531 1 56.79 ? C8 MGT 1001 B 1 HETATM 16 N N7 MGT . . . J 3 -20.97 19.195 -35.05 1 56.36 ? N7 MGT 1001 B 1 HETATM 17 C CM7 MGT . . . J 3 -20.945 19.381 -33.57 1 54.69 ? CM7 MGT 1001 B 1 HETATM 18 C C5 MGT . . . J 3 -21.775 19.667 -36.003 1 54.13 ? C5 MGT 1001 B 1 HETATM 19 C C6 MGT . . . J 3 -22.956 20.552 -35.995 1 52.46 ? C6 MGT 1001 B 1 HETATM 20 O O6 MGT . . . J 3 -23.409 21.04 -34.944 1 49.93 ? O6 MGT 1001 B 1 HETATM 21 N N1 MGT . . . J 3 -23.519 20.806 -37.191 1 53.86 ? N1 MGT 1001 B 1 HETATM 22 C C2 MGT . . . J 3 -23.039 20.288 -38.357 1 54.71 ? C2 MGT 1001 B 1 HETATM 23 N N2 MGT . . . J 3 -23.652 20.588 -39.528 1 54.99 ? N2 MGT 1001 B 1 HETATM 24 N N3 MGT . . . J 3 -21.953 19.467 -38.422 1 54.99 ? N3 MGT 1001 B 1 HETATM 25 C C4 MGT . . . J 3 -21.289 19.129 -37.295 1 55.62 ? C4 MGT 1001 B 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #