data_4U3J # _model_server_result.job_id rZNNbDqIe9wFecjajrfPTw _model_server_result.datetime_utc '2024-10-13 17:18:24' _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 4u3j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 4U3J # _exptl.entry_id 4U3J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 5 _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 112.31 _cell.angle_gamma 90 _cell.entry_id 4U3J _cell.length_a 111.909 _cell.length_b 89.573 _cell.length_c 135.508 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U3J _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 G 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 D MG MG . A MG 501 1_555 E O3G GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc2 D MG MG . A MG 501 1_555 E O2B GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc3 D MG MG . A MG 501 1_555 H O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc4 D MG MG . A MG 501 1_555 H O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc5 D MG MG . A MG 501 1_555 H O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc6 F MG MG . B MG 501 1_555 G O3G GTP . B GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc7 F MG MG . B MG 501 1_555 G O2G GTP . B GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc8 F MG MG . B MG 501 1_555 I O HOH . B HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? # _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 129 n n PG O2G GTP sing 130 n n PG O3G GTP sing 131 n n PG O3B GTP sing 132 n n O2G HOG2 GTP sing 133 n n O3G HOG3 GTP sing 134 n n O3B PB GTP sing 135 n n PB O1B GTP doub 136 n n PB O2B GTP sing 137 n n PB O3A GTP sing 138 n n O2B HOB2 GTP sing 139 n n O3A PA GTP sing 140 n n PA O1A GTP doub 141 n n PA O2A GTP sing 142 n n PA O5' GTP sing 143 n n O2A HOA2 GTP sing 144 n n O5' C5' GTP sing 145 n n C5' C4' GTP sing 146 n n C5' H5' GTP sing 147 n n C5' "H5''" GTP sing 148 n n C4' O4' GTP sing 149 n n C4' C3' GTP sing 150 n n C4' H4' GTP sing 151 n n O4' C1' GTP sing 152 n n C3' O3' GTP sing 153 n n C3' C2' GTP sing 154 n n C3' H3' GTP sing 155 n n O3' HO3' GTP sing 156 n n C2' O2' GTP sing 157 n n C2' C1' GTP sing 158 n n C2' H2' GTP sing 159 n n O2' HO2' GTP sing 160 n n C1' N9 GTP sing 161 n n C1' H1' GTP sing 162 n n N9 C8 GTP sing 163 n y N9 C4 GTP sing 164 n y C8 N7 GTP doub 165 n y C8 H8 GTP sing 166 n n N7 C5 GTP sing 167 n y C5 C6 GTP sing 168 n n C5 C4 GTP doub 169 n y C6 O6 GTP doub 170 n n C6 N1 GTP sing 171 n n N1 C2 GTP sing 172 n n N1 HN1 GTP sing 173 n n C2 N2 GTP sing 174 n n C2 N3 GTP doub 175 n n N2 HN21 GTP sing 176 n n N2 HN22 GTP sing 177 n n N3 C4 GTP sing 178 n n # _atom_sites.entry_id 4U3J _atom_sites.fract_transf_matrix[1][1] 0.008936 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003666 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011164 _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] 0.007976 _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 MG A 1 501 501 MG MG . E 5 GTP A 1 502 502 GTP GTP . F 4 MG B 1 501 501 MG MG . G 5 GTP B 1 502 502 GTP GTP . H 6 HOH A 1 601 5 HOH HOH . H 6 HOH A 2 602 8 HOH HOH . H 6 HOH A 3 603 9 HOH HOH . H 6 HOH A 4 604 11 HOH HOH . H 6 HOH A 5 605 13 HOH HOH . H 6 HOH A 6 606 16 HOH HOH . H 6 HOH A 7 607 17 HOH HOH . H 6 HOH A 8 608 18 HOH HOH . H 6 HOH A 9 609 19 HOH HOH . H 6 HOH A 10 610 21 HOH HOH . I 6 HOH B 1 601 1 HOH HOH . I 6 HOH B 2 602 2 HOH HOH . I 6 HOH B 3 603 4 HOH HOH . I 6 HOH B 4 604 6 HOH HOH . I 6 HOH B 5 605 7 HOH HOH . I 6 HOH B 6 606 10 HOH HOH . I 6 HOH B 7 607 12 HOH HOH . I 6 HOH B 8 608 14 HOH HOH . I 6 HOH B 9 609 15 HOH HOH . I 6 HOH B 10 610 20 HOH HOH . J 6 HOH C 1 601 3 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 . . . E 5 -63.83 -28.8 34.654 1 30.15 ? PG GTP 502 A 1 HETATM 2 O O1G GTP . . . E 5 -62.406 -29.261 34.472 1 25 ? O1G GTP 502 A 1 HETATM 3 O O2G GTP . . . E 5 -64.579 -29.842 35.446 1 40.53 1 O2G GTP 502 A 1 HETATM 4 O O3G GTP . . . E 5 -64.466 -28.606 33.3 1 25 ? O3G GTP 502 A 1 HETATM 5 O O3B GTP . . . E 5 -63.824 -27.417 35.484 1 56.38 ? O3B GTP 502 A 1 HETATM 6 P PB GTP . . . E 5 -64.478 -26.09 34.854 1 25 ? PB GTP 502 A 1 HETATM 7 O O1B GTP . . . E 5 -63.543 -25.488 33.835 1 33.74 1 O1B GTP 502 A 1 HETATM 8 O O2B GTP . . . E 5 -65.812 -26.419 34.232 1 29.46 ? O2B GTP 502 A 1 HETATM 9 O O3A GTP . . . E 5 -64.7 -25.053 36.065 1 25 ? O3A GTP 502 A 1 HETATM 10 P PA GTP . . . E 5 -64.962 -25.493 37.59 1 31.53 ? PA GTP 502 A 1 HETATM 11 O O1A GTP . . . E 5 -65.954 -24.511 38.152 1 39.04 1 O1A GTP 502 A 1 HETATM 12 O O2A GTP . . . E 5 -65.492 -26.904 37.702 1 33.98 ? O2A GTP 502 A 1 HETATM 13 O O5' GTP . . . E 5 -63.554 -25.315 38.356 1 32.68 ? O5' GTP 502 A 1 HETATM 14 C C5' GTP . . . E 5 -63.393 -25.695 39.709 1 33.54 ? C5' GTP 502 A 1 HETATM 15 C C4' GTP . . . E 5 -63.388 -24.495 40.653 1 34.51 ? C4' GTP 502 A 1 HETATM 16 O O4' GTP . . . E 5 -64.444 -23.617 40.33 1 32.73 ? O4' GTP 502 A 1 HETATM 17 C C3' GTP . . . E 5 -63.586 -24.928 42.098 1 34.11 ? C3' GTP 502 A 1 HETATM 18 O O3' GTP . . . E 5 -62.467 -24.593 42.886 1 35.16 ? O3' GTP 502 A 1 HETATM 19 C C2' GTP . . . E 5 -64.805 -24.181 42.596 1 30.89 ? C2' GTP 502 A 1 HETATM 20 O O2' GTP . . . E 5 -64.527 -23.564 43.832 1 31.79 ? O2' GTP 502 A 1 HETATM 21 C C1' GTP . . . E 5 -65.132 -23.187 41.49 1 30.88 ? C1' GTP 502 A 1 HETATM 22 N N9 GTP . . . E 5 -66.574 -23.153 41.191 1 25.28 ? N9 GTP 502 A 1 HETATM 23 C C8 GTP . . . E 5 -67.296 -24.127 40.554 1 29.87 ? C8 GTP 502 A 1 HETATM 24 N N7 GTP . . . E 5 -68.579 -23.712 40.454 1 32.01 ? N7 GTP 502 A 1 HETATM 25 C C5 GTP . . . E 5 -68.681 -22.485 41.01 1 31.25 ? C5 GTP 502 A 1 HETATM 26 C C6 GTP . . . E 5 -69.751 -21.618 41.169 1 31.08 ? C6 GTP 502 A 1 HETATM 27 O O6 GTP . . . E 5 -70.866 -21.93 40.762 1 33.37 ? O6 GTP 502 A 1 HETATM 28 N N1 GTP . . . E 5 -69.555 -20.404 41.786 1 28.44 ? N1 GTP 502 A 1 HETATM 29 C C2 GTP . . . E 5 -68.303 -20.053 42.242 1 31.8 ? C2 GTP 502 A 1 HETATM 30 N N2 GTP . . . E 5 -68.12 -18.878 42.841 1 34.54 ? N2 GTP 502 A 1 HETATM 31 N N3 GTP . . . E 5 -67.244 -20.922 42.08 1 28.3 ? N3 GTP 502 A 1 HETATM 32 C C4 GTP . . . E 5 -67.427 -22.118 41.473 1 26.1 ? C4 GTP 502 A 1 HETATM 33 H H4' GTP . . . E 5 -62.432 -23.979 40.566 1 41.42 ? H4' GTP 502 A 1 HETATM 34 H H3' GTP . . . E 5 -63.777 -26 42.134 1 40.93 ? H3' GTP 502 A 1 HETATM 35 H HO3' GTP . . . E 5 -62.734 -23.952 43.577 1 42.19 ? HO3' GTP 502 A 1 HETATM 36 H H2' GTP . . . E 5 -65.633 -24.882 42.701 1 37.07 ? H2' GTP 502 A 1 HETATM 37 H HO2' GTP . . . E 5 -64.6 -22.591 43.735 1 38.15 ? HO2' GTP 502 A 1 HETATM 38 H H1' GTP . . . E 5 -64.786 -22.197 41.788 1 37.06 ? H1' GTP 502 A 1 HETATM 39 H H8 GTP . . . E 5 -66.904 -25.076 40.19 1 35.84 ? H8 GTP 502 A 1 HETATM 40 H HN1 GTP . . . E 5 -70.354 -19.749 41.907 1 34.13 ? HN1 GTP 502 A 1 HETATM 41 H HN21 GTP . . . E 5 -67.199 -18.619 43.179 1 41.45 ? HN21 GTP 502 A 1 HETATM 42 H HN22 GTP . . . E 5 -68.903 -18.243 42.962 1 41.45 ? HN22 GTP 502 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 42 #