data_3WGM # _model_server_result.job_id L9xiA5iWY7aJQASWTw0G4w _model_server_result.datetime_utc '2025-07-14 11:33:02' _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 3wgm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 3WGM # _exptl.entry_id 3WGM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "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 96.11 _cell.angle_gamma 90 _cell.entry_id 3WGM _cell.length_a 44.53 _cell.length_b 89.64 _cell.length_c 66.58 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WGM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,D,G 1 1 B,E,F,H 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 ? 2 C N N ? 2 E 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 C O1G GTP . A GTP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc2 C O1B GTP . A GTP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc3 D MG MG . A MG 402 1_555 G O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc4 D MG MG . A MG 402 1_555 G O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc5 D MG MG . A MG 402 1_555 G O HOH . A HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc6 D MG MG . A MG 402 1_555 G O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc7 E O1G GTP . B GTP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc8 E O1B GTP . B GTP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc9 F MG MG . B MG 402 1_555 H O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc10 F MG MG . B MG 402 1_555 H O HOH . B HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc11 F MG MG . B MG 402 1_555 H O HOH . B HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc12 F MG MG . B MG 402 1_555 H O HOH . B HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? # _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 116 n n PG O2G GTP sing 117 n n PG O3G GTP sing 118 n n PG O3B GTP sing 119 n n O2G HOG2 GTP sing 120 n n O3G HOG3 GTP sing 121 n n O3B PB GTP sing 122 n n PB O1B GTP doub 123 n n PB O2B GTP sing 124 n n PB O3A GTP sing 125 n n O2B HOB2 GTP sing 126 n n O3A PA GTP sing 127 n n PA O1A GTP doub 128 n n PA O2A GTP sing 129 n n PA O5' GTP sing 130 n n O2A HOA2 GTP sing 131 n n O5' C5' GTP sing 132 n n C5' C4' GTP sing 133 n n C5' H5' GTP sing 134 n n C5' "H5''" GTP sing 135 n n C4' O4' GTP sing 136 n n C4' C3' GTP sing 137 n n C4' H4' GTP sing 138 n n O4' C1' GTP sing 139 n n C3' O3' GTP sing 140 n n C3' C2' GTP sing 141 n n C3' H3' GTP sing 142 n n O3' HO3' GTP sing 143 n n C2' O2' GTP sing 144 n n C2' C1' GTP sing 145 n n C2' H2' GTP sing 146 n n O2' HO2' GTP sing 147 n n C1' N9 GTP sing 148 n n C1' H1' GTP sing 149 n n N9 C8 GTP sing 150 n y N9 C4 GTP sing 151 n y C8 N7 GTP doub 152 n y C8 H8 GTP sing 153 n n N7 C5 GTP sing 154 n y C5 C6 GTP sing 155 n n C5 C4 GTP doub 156 n y C6 O6 GTP doub 157 n n C6 N1 GTP sing 158 n n N1 C2 GTP sing 159 n n N1 HN1 GTP sing 160 n n C2 N2 GTP sing 161 n n C2 N3 GTP doub 162 n n N2 HN21 GTP sing 163 n n N2 HN22 GTP sing 164 n n N3 C4 GTP sing 165 n n # _atom_sites.entry_id 3WGM _atom_sites.fract_transf_matrix[1][1] 0.022457 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002404 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011156 _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] 0.015105 _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 2 GTP A 1 401 1 GTP GTP . D 3 MG A 1 402 1 MG MG . E 2 GTP B 1 401 2 GTP GTP . F 3 MG B 1 402 2 MG MG . G 4 HOH A 1 501 1 HOH HOH . G 4 HOH A 2 502 6 HOH HOH . G 4 HOH A 3 503 7 HOH HOH . G 4 HOH A 4 504 9 HOH HOH . G 4 HOH A 5 505 15 HOH HOH . G 4 HOH A 6 506 16 HOH HOH . G 4 HOH A 7 507 17 HOH HOH . G 4 HOH A 8 508 19 HOH HOH . G 4 HOH A 9 509 20 HOH HOH . G 4 HOH A 10 510 24 HOH HOH . G 4 HOH A 11 511 27 HOH HOH . G 4 HOH A 12 512 31 HOH HOH . G 4 HOH A 13 513 32 HOH HOH . G 4 HOH A 14 514 37 HOH HOH . G 4 HOH A 15 515 38 HOH HOH . G 4 HOH A 16 516 39 HOH HOH . G 4 HOH A 17 517 40 HOH HOH . G 4 HOH A 18 518 41 HOH HOH . H 4 HOH B 1 501 2 HOH HOH . H 4 HOH B 2 502 3 HOH HOH . H 4 HOH B 3 503 4 HOH HOH . H 4 HOH B 4 504 5 HOH HOH . H 4 HOH B 5 505 8 HOH HOH . H 4 HOH B 6 506 11 HOH HOH . H 4 HOH B 7 507 12 HOH HOH . H 4 HOH B 8 508 13 HOH HOH . H 4 HOH B 9 509 14 HOH HOH . H 4 HOH B 10 510 18 HOH HOH . H 4 HOH B 11 511 21 HOH HOH . H 4 HOH B 12 512 22 HOH HOH . H 4 HOH B 13 513 23 HOH HOH . H 4 HOH B 14 514 25 HOH HOH . H 4 HOH B 15 515 26 HOH HOH . H 4 HOH B 16 516 28 HOH HOH . H 4 HOH B 17 517 29 HOH HOH . H 4 HOH B 18 518 30 HOH HOH . H 4 HOH B 19 519 33 HOH HOH . H 4 HOH B 20 520 34 HOH HOH . H 4 HOH B 21 521 35 HOH HOH . H 4 HOH B 22 522 36 HOH HOH . H 4 HOH B 23 523 42 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 GTP . . . C 2 30.063 3.778 5.761 1 21.15 ? PG GTP 401 A 1 HETATM 2 O O1G GTP . . . C 2 30.577 4.108 4.388 1 22.14 ? O1G GTP 401 A 1 HETATM 3 O O2G GTP . . . C 2 30.035 5.01 6.628 1 16.82 ? O2G GTP 401 A 1 HETATM 4 O O3G GTP . . . C 2 30.954 2.739 6.401 1 19.76 ? O3G GTP 401 A 1 HETATM 5 O O3B GTP . . . C 2 28.554 3.219 5.671 1 21.54 ? O3B GTP 401 A 1 HETATM 6 P PB GTP . . . C 2 27.588 3.435 4.407 1 12.43 ? PB GTP 401 A 1 HETATM 7 O O1B GTP . . . C 2 27.727 4.829 3.864 1 12.54 ? O1B GTP 401 A 1 HETATM 8 O O2B GTP . . . C 2 26.171 3.225 4.883 1 17.57 ? O2B GTP 401 A 1 HETATM 9 O O3A GTP . . . C 2 28.009 2.318 3.331 1 12.71 ? O3A GTP 401 A 1 HETATM 10 P PA GTP . . . C 2 27.307 2.195 1.888 1 17.1 ? PA GTP 401 A 1 HETATM 11 O O1A GTP . . . C 2 25.885 2.714 1.912 1 14.41 ? O1A GTP 401 A 1 HETATM 12 O O2A GTP . . . C 2 28.111 2.92 0.839 1 20.09 ? O2A GTP 401 A 1 HETATM 13 O O5' GTP . . . C 2 27.287 0.627 1.562 1 19.86 ? O5' GTP 401 A 1 HETATM 14 C C5' GTP . . . C 2 26.474 -0.224 2.336 1 17.89 ? C5' GTP 401 A 1 HETATM 15 C C4' GTP . . . C 2 26.008 -1.376 1.463 1 17.05 ? C4' GTP 401 A 1 HETATM 16 O O4' GTP . . . C 2 25.008 -0.872 0.6 1 15.71 ? O4' GTP 401 A 1 HETATM 17 C C3' GTP . . . C 2 27.104 -1.934 0.569 1 15.18 ? C3' GTP 401 A 1 HETATM 18 O O3' GTP . . . C 2 27.7 -3.082 1.142 1 17.36 ? O3' GTP 401 A 1 HETATM 19 C C2' GTP . . . C 2 26.365 -2.29 -0.708 1 15.81 ? C2' GTP 401 A 1 HETATM 20 O O2' GTP . . . C 2 25.978 -3.643 -0.674 1 12.8 ? O2' GTP 401 A 1 HETATM 21 C C1' GTP . . . C 2 25.1 -1.456 -0.683 1 15.48 ? C1' GTP 401 A 1 HETATM 22 N N9 GTP . . . C 2 25.123 -0.355 -1.657 1 17.44 ? N9 GTP 401 A 1 HETATM 23 C C8 GTP . . . C 2 25.988 0.71 -1.698 1 16.5 ? C8 GTP 401 A 1 HETATM 24 N N7 GTP . . . C 2 25.638 1.501 -2.74 1 14.29 ? N7 GTP 401 A 1 HETATM 25 C C5 GTP . . . C 2 24.555 0.966 -3.349 1 18.93 ? C5 GTP 401 A 1 HETATM 26 C C6 GTP . . . C 2 23.796 1.365 -4.444 1 24.48 ? C6 GTP 401 A 1 HETATM 27 O O6 GTP . . . C 2 24.081 2.393 -5.062 1 23.48 ? O6 GTP 401 A 1 HETATM 28 N N1 GTP . . . C 2 22.72 0.591 -4.84 1 21.54 ? N1 GTP 401 A 1 HETATM 29 C C2 GTP . . . C 2 22.408 -0.569 -4.152 1 21.57 ? C2 GTP 401 A 1 HETATM 30 N N2 GTP . . . C 2 21.371 -1.316 -4.53 1 18.48 ? N2 GTP 401 A 1 HETATM 31 N N3 GTP . . . C 2 23.168 -0.959 -3.066 1 17.4 ? N3 GTP 401 A 1 HETATM 32 C C4 GTP . . . C 2 24.22 -0.201 -2.673 1 18.45 ? C4 GTP 401 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #