data_5MIO # _model_server_result.job_id n0iPE--fcTBJIPCPFwX5SA _model_server_result.datetime_utc '2024-11-22 21:36:13' _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 5mio # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5MIO # _exptl.entry_id 5MIO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 5MIO _cell.length_a 51.81 _cell.length_b 229.76 _cell.length_c 293.95 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MIO _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E 1 1 B,F,G 2 1 C,H,I 3 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 4 _struct_asym.id D _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 disulf ? disulf1 C SG CYS 74 C CYS 287 1_555 C SG CYS 74 C CYS 287 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc1 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc2 D O1B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc3 C OG1 THR 142 C THR 355 1_555 H MG MG . C MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc4 C OG SER 255 C SER 468 1_555 H MG MG . C MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc5 C OD1 ASP 279 C ASP 492 1_555 H MG MG . C MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc6 H MG MG . C MG 801 1_555 I O1B ANP . C ANP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "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 PG O1G GTP doub 224 n n PG O2G GTP sing 225 n n PG O3G GTP sing 226 n n PG O3B GTP sing 227 n n O2G HOG2 GTP sing 228 n n O3G HOG3 GTP sing 229 n n O3B PB GTP sing 230 n n PB O1B GTP doub 231 n n PB O2B GTP sing 232 n n PB O3A GTP sing 233 n n O2B HOB2 GTP sing 234 n n O3A PA GTP sing 235 n n PA O1A GTP doub 236 n n PA O2A GTP sing 237 n n PA O5' GTP sing 238 n n O2A HOA2 GTP sing 239 n n O5' C5' GTP sing 240 n n C5' C4' GTP sing 241 n n C5' H5' GTP sing 242 n n C5' "H5''" GTP sing 243 n n C4' O4' GTP sing 244 n n C4' C3' GTP sing 245 n n C4' H4' GTP sing 246 n n O4' C1' GTP sing 247 n n C3' O3' GTP sing 248 n n C3' C2' GTP sing 249 n n C3' H3' GTP sing 250 n n O3' HO3' GTP sing 251 n n C2' O2' GTP sing 252 n n C2' C1' GTP sing 253 n n C2' H2' GTP sing 254 n n O2' HO2' GTP sing 255 n n C1' N9 GTP sing 256 n n C1' H1' GTP sing 257 n n N9 C8 GTP sing 258 n y N9 C4 GTP sing 259 n y C8 N7 GTP doub 260 n y C8 H8 GTP sing 261 n n N7 C5 GTP sing 262 n y C5 C6 GTP sing 263 n n C5 C4 GTP doub 264 n y C6 O6 GTP doub 265 n n C6 N1 GTP sing 266 n n N1 C2 GTP sing 267 n n N1 HN1 GTP sing 268 n n C2 N2 GTP sing 269 n n C2 N3 GTP doub 270 n n N2 HN21 GTP sing 271 n n N2 HN22 GTP sing 272 n n N3 C4 GTP sing 273 n n # _atom_sites.entry_id 5MIO _atom_sites.fract_transf_matrix[1][1] 0.019301 _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] 0.004352 _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] 0.003402 _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 4 GTP A 1 501 501 GTP GTP . E 5 MG A 1 502 502 MG MG . F 6 GDP B 1 501 501 GDP GDP . G 7 LOC B 1 502 503 LOC LOC . H 5 MG C 1 801 801 MG MG . I 8 ANP C 1 802 800 ANP ANP . # 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 GTP . . . D 4 -25.694 -58.897 25.245 1 78.66 ? PG GTP 501 A 1 HETATM 2 O O1G GTP . . . D 4 -25.274 -59.156 23.744 1 72.55 ? O1G GTP 501 A 1 HETATM 3 O O2G GTP . . . D 4 -26.984 -58.137 25.346 1 78.12 ? O2G GTP 501 A 1 HETATM 4 O O3G GTP . . . D 4 -24.653 -58.128 26.072 1 73.51 ? O3G GTP 501 A 1 HETATM 5 O O3B GTP . . . D 4 -25.875 -60.295 25.993 1 85.01 ? O3B GTP 501 A 1 HETATM 6 P PB GTP . . . D 4 -25.449 -61.723 25.426 1 89.27 ? PB GTP 501 A 1 HETATM 7 O O1B GTP . . . D 4 -25.981 -61.888 24.045 1 93.1 ? O1B GTP 501 A 1 HETATM 8 O O2B GTP . . . D 4 -25.888 -62.85 26.372 1 88.45 ? O2B GTP 501 A 1 HETATM 9 O O3A GTP . . . D 4 -23.862 -61.773 25.351 1 88.88 ? O3A GTP 501 A 1 HETATM 10 P PA GTP . . . D 4 -22.901 -63.039 25.291 1 87.19 ? PA GTP 501 A 1 HETATM 11 O O1A GTP . . . D 4 -22.178 -63.057 23.998 1 87.59 ? O1A GTP 501 A 1 HETATM 12 O O2A GTP . . . D 4 -23.731 -64.314 25.471 1 87.16 ? O2A GTP 501 A 1 HETATM 13 O O5' GTP . . . D 4 -21.938 -62.879 26.561 1 86.31 ? O5' GTP 501 A 1 HETATM 14 C C5' GTP . . . D 4 -20.52 -62.702 26.385 1 86.77 ? C5' GTP 501 A 1 HETATM 15 C C4' GTP . . . D 4 -19.835 -63.914 26.959 1 86.57 ? C4' GTP 501 A 1 HETATM 16 O O4' GTP . . . D 4 -20.418 -65.109 26.404 1 86.08 ? O4' GTP 501 A 1 HETATM 17 C C3' GTP . . . D 4 -18.333 -64 26.706 1 86.21 ? C3' GTP 501 A 1 HETATM 18 O O3' GTP . . . D 4 -17.654 -64.374 27.898 1 87.29 ? O3' GTP 501 A 1 HETATM 19 C C2' GTP . . . D 4 -18.205 -65.059 25.611 1 85.24 ? C2' GTP 501 A 1 HETATM 20 O O2' GTP . . . D 4 -17.01 -65.799 25.82 1 89.26 ? O2' GTP 501 A 1 HETATM 21 C C1' GTP . . . D 4 -19.409 -65.95 25.889 1 82.97 ? C1' GTP 501 A 1 HETATM 22 N N9 GTP . . . D 4 -19.934 -66.582 24.688 1 77.09 ? N9 GTP 501 A 1 HETATM 23 C C8 GTP . . . D 4 -20.636 -65.945 23.705 1 74.99 ? C8 GTP 501 A 1 HETATM 24 N N7 GTP . . . D 4 -20.978 -66.739 22.724 1 74.82 ? N7 GTP 501 A 1 HETATM 25 C C5 GTP . . . D 4 -20.481 -67.977 23.094 1 77.2 ? C5 GTP 501 A 1 HETATM 26 C C6 GTP . . . D 4 -20.56 -69.259 22.447 1 81.08 ? C6 GTP 501 A 1 HETATM 27 O O6 GTP . . . D 4 -21.1 -69.489 21.379 1 82.28 ? O6 GTP 501 A 1 HETATM 28 N N1 GTP . . . D 4 -19.945 -70.275 23.156 1 81.08 ? N1 GTP 501 A 1 HETATM 29 C C2 GTP . . . D 4 -19.318 -70.104 24.356 1 79.33 ? C2 GTP 501 A 1 HETATM 30 N N2 GTP . . . D 4 -18.774 -71.189 24.907 1 78.04 ? N2 GTP 501 A 1 HETATM 31 N N3 GTP . . . D 4 -19.232 -68.916 24.979 1 78.01 ? N3 GTP 501 A 1 HETATM 32 C C4 GTP . . . D 4 -19.835 -67.902 24.295 1 76.77 ? C4 GTP 501 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #